diff --git a/README.md b/README.md index b4e39a1..b4aa763 100644 --- a/README.md +++ b/README.md @@ -2,9 +2,29 @@ ### Table of Contents -1. [VariantSurvival](#variantsurvival) -2. [The shiny app](#the-shiny-app) -3. [The developers team](#the-developers-team) +1. [About](#About) +2. [VariantSurvival](#variantsurvival) +3. [The shiny app](#the-shiny-app) +4. [The developers team](#the-developers-team) +
+ + +## About +VariantSurvival is a tool to identify genotype-treatment response in neurological disseaes +
+List of currently supported neurological disorders syndroms: + +- Amyotrophic Lateral Sclerosis Spectrum Disorders +- Brain Malformations +- Cerebral Palsy +- Craniofacial Malformations +- Epilepsy +- Glaucoma and Neuro-Ophthalmology +- Intellectual Disability and Autism +- Leigh syndrome +- Parkinson disease +- Rett and Angelman-like Disorders +- Charcot-Marie-Tooth
@@ -26,10 +46,16 @@ The package can be installed in R studio using the following command: ``` #install.packages('devtools') #install devtools package library(devtools) -devtools::install_github("collaborativebioinformatics/VariantSurvival/VariantSurvival_package") +devtools::install_github("collaborativebioinformatics/VariantSurvival/variantsurvival") ``` Note: All required packages will be installed automatically when installing "VariantSurvival". +### Demonstration +``` +VariantSurvival::VariantSurvival(demo="TRUE") +``` + + ### Running your data analysis * WIP: what input to load into VariantSurvival: [VCF file](https://github.com/collaborativebioinformatics/VariantSurvival/blob/main/docs/preprocessing/prepareVCF.md), study groups metadata @@ -42,8 +68,6 @@ VariantSurvival::VariantSurvival(vcffile="variant_file_.vcf", metadatafile= "met ``` - - ## The developers team * Ahmad Al Khleifat [![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/AhmadAlKhleifat.svg?style=social&label=Follow%20%40AhmadAlKhleifat)](https://twitter.com/AhmadAlKhleifat) diff --git a/Refrences.txt b/Refrences.txt deleted file mode 100644 index 627c0f0..0000000 --- a/Refrences.txt +++ /dev/null @@ -1,15 +0,0 @@ -Winston Chang , Joe Cheng,JJ Allaire, Carson Sievert , Barret Schloerke , Yihui Xie, et al. shiny: Web Application Framework for R (2022). https://github.com/rstudio/shiny -Winston Chang, Barbara Borges Ribeiro (2021). https://github.com/rstudio/shinydashboard. -lboukadel Kassambara [aut, cre], Marcin Kosinski [aut], Przemyslaw Biecek [aut], Scheipl Fabian. survminer: Drawing Survival Curves using 'ggplot2'. 2021. https://rpkgs.datanovia.com/survminer/index.html -Grolemund G, Wickham H (2011). “Dates and Times Made Easy with lubridate.” Journal of Statistical Software, 40(3), 1–25. https://www.jstatsoft.org/v40/i03/. -Yihui Xie [aut, cre], Joe Cheng [aut], Xianying Tan [aut], JJ Allaire [ctb], Maximilian Girlich [ctb], Greg Freedman Ellis et al. 2022. DT: A Wrapper of the JavaScript Library 'DataTables'. https://github.com/rstudio/DT -Terry M. Therneau, Patricia M. Grambsch (2000). Modeling Survival Data: Extending the Cox Model. Springer, New York. ISBN 0-387-98784-3. -Therneau T (2022). A Package for Survival Analysis in R. R package version 3.4-0, https://CRAN.R-project.org/package=survival. -Knaus BJ, Grünwald NJ (2017). “VCFR: a package to manipulate and visualize variant call format data in R.” Molecular Ecology Resources, 17(1), 44–53. ISSN 757, http://dx.doi.org/10.1111/1755-0998.12549. -Wickham H, Hester J, Bryan J (2022). readr: Read Rectangular Text Data. https://readr.tidyverse.org, https://github.com/tidyverse/readr. -Wickham H, Bryan J (2022). readxl: Read Excel Files. https://readxl.tidyverse.org, https://github.com/tidyverse/readxl. -Sjoberg D, Whiting K, Curry M, Lavery J, Larmarange J (2021). “Reproducible Summary Tables with the gtsummary Package.” The R Journal, 13, 570-580. doi:10.32614/RJ-2021-053, https://doi.org/10.32614/RJ-2021-053. -Daniel D. Sjoberg . ggsurvfit: Easy and Flexible Time-to-Event Figures. 2022.https://github.com/ddsjoberg/ggsurvfit, -Wickham H, François R, Henry L, Müller K (2022). dplyr: A Grammar of Data Manipulation. https://dplyr.tidyverse.org, https://github.com/tidyverse/dplyr. -Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, Grolemund G, Hayes A, Henry L, Hester J, Kuhn M, Pedersen TL, Miller E, Bache SM, Müller K, Ooms J, Robinson D, Seidel DP, Spinu V, Takahashi K, Vaughan D, Wilke C, Woo K, Yutani H (2019). “Welcome to the tidyverse.” Journal of Open Source Software, 4(43), 1686. doi:10.21105/joss.01686. -Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4, https://ggplot2.tidyverse.org. \ No newline at end of file diff --git a/VariantSurvival_package/R/VariantSurvival.R b/VariantSurvival_package/R/VariantSurvival.R deleted file mode 100644 index 8eaa1fd..0000000 --- a/VariantSurvival_package/R/VariantSurvival.R +++ /dev/null @@ -1,820 +0,0 @@ -#' VariantSurvival -#' -#' @param vcffile path to the vcf file containing the Structural variant data -#' @param metadatafile path to the txt file containing the samples metadata -#' @param demo true or false -#' -#' @return -#' @export -#' - -VariantSurvival <- function(vcffile, metadatafile,demo=FALSE){ - install_load_requirements() - #demo or input files - if (demo==TRUE){ - vcffile_demo <- "merged.filtered.vcf" - vcf <- vcfR::read.vcfR(vcffile_demo, verbose = FALSE) - metadata_demo <-"metadata.xlsx" - metadata <- readxl::read_excel(metadata_demo) - metadata <- na.omit(metadata) - } else if (demo==FALSE){ - vcf <- vcfR::read.vcfR(vcffile, verbose = FALSE) - metadata <- readxl::read_excel(metadatafile) - metadata <- na.omit(metadata) - - } - disease_gene <- read_excel("disease_gene.xlsx") - days_year <- 365.25 - - ui <- bootstrapPage( - navbarPage(theme = shinytheme("flatly"), - collapsible = TRUE, - HTML('VariantSurvival'), - id="nav", - windowTitle ="VariantSurvival", - tabPanel("Select Target Gene", - sidebarLayout( - sidebarPanel( - pickerInput(inputId ="disease_n", - label = "Select the disease of interest:", - choices = c(colnames(disease_gene), "N/A"), - selected = "N/A" - ), - selectInput(inputId = "ids", - label = "Select the participant ID:", - choices = c(colnames(metadata), "N/A"), - selected = "N/A" - ), - selectInput(inputId = "time", - label = "Select the time factor:", - choices = c(colnames(metadata), "N/A"), - selected = "N/A" - ), - radioButtons(inputId = "time_unit", - label = "Time factor unit:", - choices = c("years", "days"), - inline = TRUE - ), - span(shiny::tags$i( - h6("Based on literature the following genes are - associated with the disease mechanism") - ), - style="color:#045a8d"), - selectInput(inputId = "target_gene", - label = "Gene of interest:", - choices = NULL, - selected = FALSE - ), - span(shiny::tags$i( - h6("The following selections must refer to binary factors")), - style="color:#045a8d"), - selectInput(inputId = "group", - label = "Select the clinical trial groups factor:", - choices =c(colnames(metadata), "N/A"), - selected = "N/A" - ), - selectInput(inputId = "event", - label = "Select the alive/dead factor:", - choices = c(colnames(metadata), "N/A"), - selected = "N/A" - ) - ), - mainPanel( - tabBox( - selected = "Summary", - tabPanel("Summary", - span(DT::dataTableOutput("summ_table")) - ), - tabPanel("Histogram", - span(shiny::tags$i( - h2("Structural Variants Distribution"))), - shinycssloaders::withSpinner( - plotOutput(outputId = "histogram")) - ), - tabPanel("Table", - selectInput(inputId = "table_cols", - label = "Include columns (optional)", - choices = NULL, - selected = FALSE, - multiple = TRUE), - span(DT::dataTableOutput("table")) - ) - ) - ) - ) - ), - tabPanel("Survival Analysis", - mainPanel( - span(shiny::tags$i( - h2("Kaplan–Meier")), - # to enable/disable the n_svs_min & n_svs_max fields, - #this should be added at the panel level - shinyjs::useShinyjs(), - tabBox( - tabPanel("Null model", - fluidRow(column(12, - #div(style = "height:70px; Topleft"), - shinycssloaders::withSpinner( - plotOutput(outputId = "null_model_km"))), - column(6, - #div(style = "height:200px; Bottomleft"), - checkboxInput("life_table_null_model", - "Display life table", - value = FALSE), - box(id = "myBox", title = "", #width = '200px', - span(DT::dataTableOutput("null_model_life_table")))) - ) - ), - tabPanel("Multiple model", - fluidRow(column(12, - div(style = "height:70px; Topleft"), - dropdownButton( - checkboxInput("all_n_svs", - "Include all counts", - value = TRUE - ), - selectInput(inputId = "n_svs_min", - label = "min", - choices = NULL, - selected = FALSE - ), - selectInput(inputId = "n_svs_max", - label = "max", - choices = NULL, - selected = FALSE - ), - checkboxGroupInput("km_feat", - "Plot layout options:", - choices = c("confidence interval" = "conf_itv", - "risk table" = "risk_table", - "y grid line" = "grid_line")), - circle = TRUE, - status = "danger", - icon = icon("gear"), width = "200", - tooltip = tooltipOptions(title = "Click to see inputs !") - ), - shinycssloaders::withSpinner( - plotOutput(outputId = "plot_km",width = "100%")) - ) - ), - fluidRow(column(12, div(style = "height:200px; Bottomleft"), - checkboxInput("life_table_multiple_model", - "Display life table", - value = FALSE), - box(id = "myBox_mm", title = "", width = '200px', - span(DT::dataTableOutput("multiple_model_life_table")))) - ) - ) - ) - ) - ) - ), - tabPanel("Cox regression", - span(shiny::tags$i( - h3("Cox regression table")), - style="color:#045a8d", - shinyjs::useShinyjs(), - tabBox( - tabPanel("Standard model", - dropdownButton( - checkboxInput("cox_reg_td", - "With time-dependent covariates", - value = TRUE), - selectizeInput(inputId = "sel_cov", - label = "Select categorical covariates", - # SV_bin is added by us, 0/1 without/with SV - choices = NULL, - selected = FALSE, - multiple = TRUE - ), - selectizeInput(inputId = "sel_cov_cont", - label = "Select continuous covariates", - choices = NULL, - selected = FALSE, - multiple = TRUE - ), - selectInput(inputId = "sel_strata", - label = "Select strata covariate (optional)", - choices = NULL), - circle = TRUE, - status = "danger", - icon = icon("gear"), width = "300", - tooltip = tooltipOptions(title = "Click to see inputs !")), - span(DT::dataTableOutput("table3")) - - ), - tabPanel("Multiple model", - checkboxInput("cox_reg_td", - "With time-dependent covariates", - value = TRUE), - selectizeInput(inputId = "sel_cov", - label = "Select categorical covariates", - # SV_bin is added by us, 0/1 without/with SV - choices = NULL, - selected = FALSE, - multiple = TRUE - ), - selectizeInput(inputId = "sel_cov_cont", - label = "Select continuous covariates", - choices = NULL, - selected = FALSE, - multiple = TRUE - ), - selectInput(inputId = "sel_strata", - label = "Select strata covariate (optional)", - choices = NULL) - ) - ) - ) - ) - ) - ) - - - server <- function(input, output, session) { - gene_ids_table <- read.csv(file = 'ensembleTogenes.csv') - rownames(gene_ids_table) <- gene_ids_table$ensembleID - # get disease_n input and update the genes list accordingly - observeEvent(input$disease_n, { - if(input$disease_n!= "N/A"){ - genes_list <- c(get_disease_gene_list(disease_gene,input$disease_n)) - disease_genes_names <- gene_ids_table$GeneName - updateSelectizeInput(session, - input = "target_gene", - choices = genes_list, - selected = NULL) - } - }) - - - observe({ if(input$disease_n != "N/A" - & input$ids != "N/A" - &input$time != "N/A"){ - genes_with_svs_in_sample <- apply(vcf@fix, 1, getGeneName,gene_ids_table) - sample_names <- colnames(vcf@gt)[-1] - disease_genes_names <- gene_ids_table$GeneName - output$summ_table <- DT::renderDataTable({ - # count dataframe with patient_ids in rows and gene_ids in columns - count_df <- CountSVsDf(length(disease_genes_names), - length(sample_names), - disease_genes_names, - sample_names, - genes_with_svs_in_sample, - vcf, - input$ids) - new_md <- RemoveNAs(metadata, input$time) %>% rename(ids = input$ids) - # what happen if the input$target_gene is not in the vcf file? - new_df <- subset(count_df, ids %in% new_md$ids) - count <- as.data.frame(apply(new_df[,-1], 2, function(c)sum(c!=0))) - colnames(count) <- "Count of patients with SVs" - count <- count %>% arrange(desc(count)) - count - }) - } - }) - - reactive_no_NAs_metadata <- reactive({ - if(checkInput(input)){ - disease_genes_names <- gene_ids_table$GeneName - sample_names <- colnames(vcf@gt)[-1] # ignore VCF genotype information - # genes are repeated since a single gene can have more than one SV. - genes_with_svs_in_sample <- apply(vcf@fix, - 1, - getGeneName, - gene_ids_table) - # count dataframe with patient_ids in rows and gene_ids in columns - count_df <- CountSVsDf(length(disease_genes_names), - length(sample_names), - disease_genes_names, - sample_names, - genes_with_svs_in_sample, - vcf, - input$ids) - new_md <- (RemoveNAs(metadata, input$time) - %>% rename(ids = input$ids, - trial_group_bin = input$group, - time = input$time, - event = input$event) - ) - # what happen if the input$target_gene is not in the vcf file? - new_df <- (subset(count_df, ids %in% new_md$ids) - %>% rename(SV_count_per_gene = input$target_gene) - ) - no_na_df <- merge(new_df, new_md, by = "ids") - no_na_df <- transform(no_na_df, - time = as.numeric(time), - event = as.numeric(event), - SV_count_per_gene = as.numeric(SV_count_per_gene) - ) - no_na_df <- (no_na_df - %>% mutate(SV_bin = ifelse(new_df$SV_count_per_gene>0, 1, 0) - ) - %>% mutate(trial_group = ifelse(trial_group_bin=="0", - "Placebo", - "Treatment") - ) - %>% mutate(SV = ifelse(SV_bin=="0", "with", "without") - ) - ) - if(input$time_unit == 'years'){ - no_na_df$time_days <- floor(no_na_df[["time"]] * days_year) - } else{ - no_na_df$time_years <- no_na_df[["time"]] / days_year - } - no_na_df - } - } - ) - - ## output - histogram ## - output$histogram <- renderPlot( - { - if(checkInput(input)){ - new_df <- reactive_no_NAs_metadata() - # get a dataframe with counts - svs_gene_input_df <- new_df[c("ids", "trial_group", "SV_count_per_gene")] - legend_title <- "Group" - ggplot(svs_gene_input_df, aes(SV_count_per_gene, fill=trial_group)) + - geom_histogram(binwidth=1) + - stat_bin(binwidth=1, - geom='text', - color='white', - aes(label=after_stat(if_else(condition = count>0, - as.character(count), ""))), - position=position_stack(vjust = 0.5)) + - xlab("Number of SVs in target gene") + ylab("Frequency") + - theme(text = element_text(size = 20), - panel.background = element_rect(fill = "white", - colour = "white"), - axis.line = element_line(colour = "black"), - panel.grid.major = element_blank(), - panel.grid.minor = element_blank(), - legend.position="top" - ) + - scale_fill_manual(legend_title, values=c("#8B1D4D", "#5275A6")) - } - }, - height = 500, - width = 700 - ) - - observe({ - if(checkInput(input) & !is.null(input$target_gene)){ - svs_gene_input_df <- reactive_no_NAs_metadata() - # renaming back to original column names, so it's not confusing for the user. - # maybe not the best approach - rename_cols <- c("ids", "trial_group_bin", "time", "event") - rename_cols_with <- c(input$ids, input$group, input$time, input$event) - names(svs_gene_input_df)[names(svs_gene_input_df) %in% rename_cols]<- rename_cols_with - coln_list <- colnames(svs_gene_input_df) - coln_list <- coln_list[!(coln_list %in% c(input$ids,"SV_count_per_gene"))] - updateSelectizeInput(session, - input = "table_cols", - choices = coln_list, - selected = NULL) - } - }) - - observe({ - if(checkInput(input)){ - svs_gene_input_df <- reactive_no_NAs_metadata() - # renaming back to original column names, so it's not confusing for the user. - # maybe not the best approach - rename_cols <- c("ids", "trial_group_bin", "time", "event") - rename_cols_with <- c(input$ids, input$group, input$time, input$event) - names(svs_gene_input_df)[names(svs_gene_input_df) %in% rename_cols]<- rename_cols_with - if(any(!is.na(input$table_cols))){ - output$table <- DT::renderDataTable({ - col_names_list <- c(c(input$ids, "SV_count_per_gene"), - input$table_cols) - svs_gene_input_df <- as_tibble(svs_gene_input_df[col_names_list]) - svs_gene_input_df - }) - } - else{ - output$table <- DT::renderDataTable({ - svs_gene_input_df <- as_tibble(svs_gene_input_df[c(input$ids, "SV_count_per_gene")]) - colnames(svs_gene_input_df) <- c("ID", "SV count in gene of interest") - svs_gene_input_df - }) - } - } - }) - - observe({ - if(checkInput(input)){ - svs_gene_input_df <- reactive_no_NAs_metadata() - null_model <- survfit(Surv(time, event)~1, - data = svs_gene_input_df, - type = "kaplan-meier") - output$null_model_km <- renderPlot({ - ggsurvplot_combine(list(null_model), - data=no_na_df, - risk.table = FALSE, - conf.int = FALSE, - conf.int.style = "step", - risk.table.y.text = FALSE, - xlab = "Years", - ylab = "Overall survival probability", - legend = "none", - ggtheme = theme( - text = element_text(size = 20), - panel.background = element_rect(fill = "white", - colour = "white"), - axis.line = element_line(colour = "black"), - panel.grid.major.y = element_line(colour='white'), - panel.grid.minor.y = element_line(colour='white'), - # legend.position = c(0.2, 0.5) - )) - }, - height = 500, - width = 700) - - observeEvent(input$life_table_null_model, { - if(input$life_table_null_model == FALSE){ - shinyjs::hide(id = "myBox") - } - else if(input$life_table_null_model==TRUE){ - shinyjs::show(id = "myBox") - output$null_model_life_table <- DT::renderDataTable({ - as_tibble(round_df(as.data.frame(surv_summary(null_model)), 3)) - }) - } - }) - } - }) - - observe({ - if(checkInput(input)){ - risk_table = FALSE - conf_itv = FALSE - grid_line = "white" - if(!is.null(input$km_feat)){ - if("conf_itv" %in% input$km_feat){ - conf_itv = TRUE} - if("risk_table" %in% input$km_feat){ - risk_table = TRUE} - if("grid_line" %in% input$km_feat){ - grid_line = "grey"} - } - svs_gene_input_df <- reactive_no_NAs_metadata() - if (input$all_n_svs == FALSE - & input$n_svs_min!= "" - & input$n_svs_max!= ""){ - if (input$n_svs_max > input$n_svs_min){ - n_svs_min = as.numeric(input$n_svs_min) - n_svs_max = as.numeric(input$n_svs_max) - sub <- (svs_gene_input_df$SV_count_per_gene >= n_svs_min - & svs_gene_input_df$SV_count_per_gene <= n_svs_max) - svs_gene_input_df <- svs_gene_input_df[sub,] - } - } - groups_df <- (unique(svs_gene_input_df[c("SV_bin", "trial_group_bin")]) - %>% arrange(SV_bin, trial_group_bin)) - lables <- c() - cols <- c() - for (row in 1:nrow(groups_df)){ - sv_bin <- groups_df[row, "SV_bin"] - trial_g <- groups_df[row, "trial_group_bin"] - if (sv_bin == 0){ - if (trial_g == 0){ - lables <- c(lables, "without sv - placebo") - cols <- c(cols, "Violetred2") - } - else if (trial_g == 1){ - lables <- c(lables, "without sv - treatment") - cols <- c(cols, "turquoise3") - } - } - if (sv_bin == 1){ - if (trial_g == 0){ - lables <- c(lables, "with sv - placebo") - cols <- c(cols, "Violetred4") - } - else if (trial_g == 1){ - lables <- c(lables, "with sv - treatment") - cols <- c(cols, "steelblue") - } - } - } - n_sv_groups <- unique(svs_gene_input_df[["SV_bin"]]) - # can it happen that there are more than 1 patient groups? - if(length(n_sv_groups) == 2){ - # generate survival curve objects for each group - sc_without <- survfit2(Surv(time, event)~trial_group_bin, - data = svs_gene_input_df, - subset=(SV_bin==0), - type = "kaplan-meier") - sv_with <- survfit2(Surv(time, event)~trial_group_bin, - data = svs_gene_input_df, - subset=(SV_bin==1), - type = "kaplan-meier") - surv_fit_list <- list("with SV" = sv_with, "without SV" = sc_without) - } - else if(length(n_sv_groups) ==1){ - if (n_sv_groups == 0){ - type = "without"} - else if (n_sv_groups == 1){ - type = "with"} - temp <- paste(type , " SV") - sc <- survfit2(Surv(time, event)~trial_group_bin, - data = svs_gene_input_df, - type = "kaplan-meier") - surv_fit_list <- list(temp = sc) - } - - output$plot_km <- renderPlot({ - ggsurvplot_combine(surv_fit_list, - data=svs_gene_input_df, - risk.table = risk_table, - conf.int = conf_itv, - conf.int.style = "step", - risk.table.y.text = FALSE, - xlab = toTitleCase(input$time_unit), - ggtheme = theme( - text = element_text(size = 20), - panel.background = element_rect(fill = "white", - colour = "white"), - axis.line = element_line(colour = "black"), - panel.grid.major.y = element_line(colour=grid_line), - panel.grid.minor.y = element_line(colour=grid_line), - # legend.position = c(0.2, 0.5) - ), - legend = "right", - legend.title = "Group", - legend.labs =lables, - palette = cols - )}, - height = 600, - width = 1000) - } - else{ - output$plot_km <- renderText({ "Missing input data"}) - } - }) - - inputs_react <- reactive({list(input$event, - input$time, - input$ids, - input$target_gene - )}) - # hide the event, time and ids covariates from the covariates and strata - # drop-down - observeEvent(inputs_react(), - {if(checkInput(input)){ - svs_gene_input_df <- reactive_no_NAs_metadata() - svs_levels <- unique(svs_gene_input_df["SV_count_per_gene"])$SV_count_per_gene - cov_list <- c(get_cov_list(metadata, input), "SV_bin") - # update the covariate drop down - updateSelectizeInput(session, - input = "sel_cov", - choices = cov_list, - options = list(create = TRUE)) - # update the strata drop down, this field is optional - updateSelectizeInput(session, - input = "sel_cov_cont", - choices = cov_list, - options = list(create = TRUE)) - updateSelectizeInput(session, - input = "sel_strata", - choices = c(cov_list, c("SV_bin","N/A")), - selected = "N/A") - } - } - ) - - observeEvent(input$all_n_svs, { - if (checkInput(input)){ - if (input$all_n_svs == FALSE){ - shinyjs::enable("n_svs_min") - shinyjs::enable("n_svs_max") - svs_gene_input_df <- reactive_no_NAs_metadata() - svs_levels <- unique(svs_gene_input_df["SV_count_per_gene"])$SV_count_per_gene - updateSelectizeInput(session, - input = "n_svs_min", - choices = sort(svs_levels)) - } - else { - shinyjs::disable("n_svs_min") - shinyjs::disable("n_svs_max") - } - } - } - ) - - observeEvent(input$n_svs_min, { - if (checkInput(input)){ - if (input$all_n_svs == FALSE & input$n_svs_min!=""){ - svs_gene_input_df <- reactive_no_NAs_metadata() - svs_levels <- unique(svs_gene_input_df["SV_count_per_gene"])$SV_count_per_gene - max_levels <- sort(svs_levels[svs_levels >= as.numeric(input$n_svs_min)]) - updateSelectizeInput(session, - input = "n_svs_max", - choices = max_levels) - } - } - } - ) - - - output$table3 <- DT::renderDataTable({ - if(checkInput(input) & (any(!is.na(input$sel_cov)) | any(!is.na(input$sel_cov_cont)))){ - covariates <- c() - input_df <- reactive_no_NAs_metadata() - if (any(!is.na(input$sel_cov_cont))){ - input_cov_cont <- map_col_names(input, input$sel_cov_cont) - input_df[input_cov_cont] <- sapply(input_df[input_cov_cont],as.numeric) - covariates <- c(covariates, input_cov_cont) - } - if(any(!is.na(input$sel_cov))){ - input_cov_cat <- map_col_names(input, input$sel_cov) - input_df[input_cov_cat] <- sapply(input_df[input_cov_cat],as.character) - covariates <- c(covariates, input_cov_cat) - } - formulaString <- paste("Surv(time, event) ~", paste(covariates, collapse="+")) - x3 <- (coxph(as.formula(formulaString), data=input_df) - %>% tbl_regression(exp = TRUE)) - proport_hazard_assump <- cox.zph(cox_reg.std) - t3 <-as_tibble(x3) - t3 - } - }) - } - - # Run the application - shinyApp(ui = ui, server = server) -} - - -############# Helper functions ################### -install_load_requirements<- function() { - if (!require("shiny")) install.packages("shiny") - if (!require("shinyjs")) install.packages("shinyjs") - if (!require("shinyWidgets")) install.packages("shinyWidgets") - if (!require("shinythemes")) install.packages("shinythemes") - if (!require("shinycssloaders")) install.packages("shinycssloaders") - if (!require("shinydashboard")) install.packages("shinydashboard") - if (!require("DT")) install.packages("DT") - if (!require("dplyr")) install.packages("dplyr") - if (!require("tidyverse")) install.packages("tidyverse") - if (!require("vcfR")) install.packages("vcfR") - if (!require("readr")) install.packages("readr") - if (!require("ggsurvfit")) install.packages("ggsurvfit") - if (!require("survival")) install.packages("survival") - if (!require("ggplot2")) install.packages("ggplot2") - if (!require("survminer")) install.packages("survminer") - if (!require("lubridate")) install.packages("lubridate") - if (!require("gtsummary")) install.packages("gtsummary") - if (!require("tools")) install.packages("tools") - library(shiny) - library(shinyjs) - library(shinydashboard) - library(shinythemes) - library(shinyWidgets) - library(shinycssloaders) - library(DT) - library(dplyr) - library(tidyverse) - library(vcfR) - library(readr) - library(readxl) - library(ggsurvfit) - library(survival) - library(ggplot2) - library(survminer) - library(lubridate) - library(gtsummary) -} - - -#' `get_disease_gene_list` parses an existing .txt -#' file containing all known target genes associated -#' with the selected disease. -#' @param input_disease: input disease selection -#' @return genes_list -get_disease_gene_list <- function(disease_gene, input_disease) { - genes_list <-( na.omit(disease_gene[,input_disease]) - %>% rename(genes = input_disease)) - return(genes_list$genes) -} - - -#' `checkInput` -#' @param info -#' @return -checkInput <- function(input) { - if (input$ids != "N/A" - & input$time != "N/A" - & input$group != "N/A" - & input$event != "N/A" - & input$target_gene != "N/A"){ - return(TRUE) - }else{ - return(FALSE) - } -} - - -#' `getGeneName` -#' @param info -#' @return -getGeneName <- function(info, geneIDS) { - x <- str_extract(info['INFO'], "(?<=ensembl_gene_id=)[^;]+") - return(geneIDS[x,]$GeneName) -} - - -get_cov_list <- function(metadata, input) { - inputs_list <- c(input$event, input$time, input$ids) - cov_list <- colnames(metadata) - cov_list <- cov_list[!(cov_list %in% inputs_list)] - return(cov_list) -} - - -#' `CountSVsDf` -#' @param ncol -#' @param nrow -#' @param disease_genes_names -#' @param sample_names -#' @param genes_with_svs_in_sample -#' @param vcf -#' @return -CountSVsDf <- function(ncol, nrow, - disease_genes_names, - sample_names, - genes_with_svs_in_sample, - vcf, - ids_col){ - sample_disease_gene_df <- data.frame(matrix(0, ncol = ncol, nrow = nrow)) - colnames(sample_disease_gene_df) <- disease_genes_names - rownames(sample_disease_gene_df) <- sample_names - - for (sv_idx in 1:length(genes_with_svs_in_sample)) { - # if the sv is in a gene of interest - sv_gene_name <- genes_with_svs_in_sample[sv_idx] - if(is.na(sv_gene_name)) - next - for(individual_idx in 1:length(sample_names)){ - indiv_id <- sample_names[individual_idx] - gt <- vcf@gt[sv_idx, indiv_id] - if(!is.na(gt)) - { - sample_disease_gene_df[indiv_id, sv_gene_name] %+=% 1 - } - } - } - sample_disease_gene_df <- (rownames_to_column(sample_disease_gene_df,ids_col) - %>% rename(ids = ids_col)) - return(sample_disease_gene_df) -} - - -#' `RemoveNAs` removes all rows with Na -#' entries in the time factor column. -#' @param df: metadata data frame -#' @param time_col: time factor input -#' @return -RemoveNAs <- function(df, time_col) { - entries <- df[[time_col]] - nas_entries <- is.na(entries) - NAs_entries <- entries=="NA" - if (sum(nas_entries) > 0){ - return(df[!nas_entries,]) - } else if (sum(NAs_entries) > 0){ - return(df[!NAs_entries,]) - } else { - return(df) - } -} - -round_df <- function(x, digits) { - # round all numeric variables - # x: data frame - # digits: number of digits to round - numeric_columns <- sapply(x, mode) == 'numeric' - x[numeric_columns] <- round(x[numeric_columns], digits) - x -} - - -map_col_names <- function(input, cov_list){ - if(input$event %in% cov_list){ - cov_list <- str_replace(cov_list, - input$event, - "event")} - if(input$group %in% cov_list){ - cov_list <- str_replace(cov_list, - input$group, - "trial_group_bin") - } - return(cov_list) -} - - -#' implementation of += operator -#' https://stackoverflow.com/questions/5738831/ -`%+=%` <- function(e1,e2) eval.parent(substitute(e1 <- e1 + e2)) diff --git a/VariantSurvival_package/R/disease_gene.xlsx b/VariantSurvival_package/R/disease_gene.xlsx deleted file mode 100644 index 17b31ac..0000000 Binary files a/VariantSurvival_package/R/disease_gene.xlsx and /dev/null differ diff --git a/VariantSurvival_package/R/ensembleTogenes.csv b/VariantSurvival_package/R/ensembleTogenes.csv deleted file mode 100644 index 95b9e1e..0000000 --- a/VariantSurvival_package/R/ensembleTogenes.csv +++ /dev/null @@ -1,57 +0,0 @@ -GeneName,ensembleID -ANG,ENSG00000214274 -CHMP2B,ENSG00000083937 -DAO,ENSG00000110887 -DCTN1,ENSG00000204843 -FIG4,ENSG00000112367 -FUS,ENSG00000089280 -NEFH,ENSG00000100285 -OPTN,ENSG00000123240 -PFN1,ENSG00000108518 -PON1,ENSG00000005421 -PON2,ENSG00000105854 -PON3,ENSG00000105852 -PRPH,ENSG00000135406 -SETX,ENSG00000107290 -SOD1,ENSG00000142168 -SQSTM1,ENSG00000161011 -TARDBP,ENSG00000120948 -TREM2,ENSG00000095970 -UBQLN2,ENSG00000188021 -VAPB,ENSG00000124164 -APP,ENSG00000142192 -PSEN1,ENSG00000080815 -PSEN2,ENSG00000143801 -S100A9,ENSG00000163220 -CR1,ENSG00000203710 -BIN1,ENSG00000136717 -CLU,ENSG00000120885 -CTNNA3,ENSG00000183230 -DNMBP,ENSG00000107554 -SORL1,ENSG00000137642 -BACE1,ENSG00000186318 -PICALM,ENSG00000073921 -GAB2,ENSG00000033327 -LRP6,ENSP00000261349 -ADAM10,ENSG00000137845 -ABCA7,ENSG00000064687 -CD33,ENSG00000105383 -TOMM40,ENSG00000130204 -PARK7,ENSG00000116288 -PARK9,ENST00000326735 -GBA,ENSG00000177628 -SNCA,ENSG00000145335 -PARK2,ENST00000366898 -LRRK2,ENSG00000188906 -SIGMAR1,ENSG00000147955 -VCP,ENSG00000165280 -GRN,ENSG00000030582 -MAPT,ENSG00000186868 -ALS2,ENSG00000003393 -TAF15,ENSG00000270647 -HNRNPA1,ENSG00000135486 -UCHL1,ENSG00000154277 -PINK1,ENSG00000158828 -PLA2G6,ENSG00000184381 -FBXO7,ENSG00000100225 -VPS35,ENSG00000069329 diff --git a/VariantSurvival_package/R/merged.filtered.vcf b/VariantSurvival_package/R/merged.filtered.vcf deleted file mode 100644 index 6d1266d..0000000 --- a/VariantSurvival_package/R/merged.filtered.vcf +++ /dev/null @@ -1,274 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##reference=/illumina/development/Isis/Genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##ALT= -##ALT= -##ALT= -##ALT= -##ALT= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##workflow_type=Illumina_WGS_Services -##workflow_version=v2.0.3 -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##bcftools_normVersion=1.7+htslib-1.7-2 -##bcftools_normCommand=norm -cx -f hg19.fa -Ov LP6005878-DNA_A01.SV.vcf.gz; Date=Wed Oct 12 04:23:03 2022 -##bcftools_mergeVersion=1.7+htslib-1.7-2 -##bcftools_mergeCommand=merge LP6005878-DNA_A01.SV.vcf.gz LP6005878-DNA_A02.SV.vcf.gz LP6005878-DNA_A03.SV.vcf.gz LP6005878-DNA_A04.SV.vcf.gz LP6005878-DNA_A05.SV.vcf.gz LP6005878-DNA_A06.SV.vcf.gz LP6005878-DNA_A07.SV.vcf.gz LP6005878-DNA_A08.SV.vcf.gz LP6005878-DNA_A09.SV.vcf.gz LP6005878-DNA_B01.SV.vcf.gz LP6005878-DNA_B02.SV.vcf.gz LP6005878-DNA_B03.SV.vcf.gz LP6005878-DNA_B04.SV.vcf.gz LP6005878-DNA_B05.SV.vcf.gz LP6005878-DNA_B06.SV.vcf.gz LP6005878-DNA_B07.SV.vcf.gz LP6005878-DNA_B08.SV.vcf.gz LP6005878-DNA_B09.SV.vcf.gz LP6005878-DNA_C01.SV.vcf.gz LP6005878-DNA_C02.SV.vcf.gz LP6005878-DNA_C03.SV.vcf.gz LP6005878-DNA_C04.SV.vcf.gz LP6005878-DNA_C05.SV.vcf.gz LP6005878-DNA_C06.SV.vcf.gz LP6005878-DNA_C07.SV.vcf.gz LP6005878-DNA_C08.SV.vcf.gz LP6005878-DNA_C09.SV.vcf.gz LP6005878-DNA_D01.SV.vcf.gz LP6005878-DNA_D02.SV.vcf.gz LP6005878-DNA_D03.SV.vcf.gz LP6005878-DNA_D04.SV.vcf.gz LP6005878-DNA_D05.SV.vcf.gz LP6005878-DNA_D06.SV.vcf.gz LP6005878-DNA_D07.SV.vcf.gz LP6005878-DNA_D08.SV.vcf.gz LP6005878-DNA_E01.SV.vcf.gz LP6005878-DNA_E02.SV.vcf.gz LP6005878-DNA_E03.SV.vcf.gz LP6005878-DNA_E04.SV.vcf.gz LP6005878-DNA_E05.SV.vcf.gz LP6005878-DNA_E06.SV.vcf.gz LP6005878-DNA_E07.SV.vcf.gz LP6005878-DNA_E08.SV.vcf.gz LP6005878-DNA_F01.SV.vcf.gz LP6005878-DNA_F02.SV.vcf.gz LP6005878-DNA_F03.SV.vcf.gz LP6005878-DNA_F04.SV.vcf.gz LP6005878-DNA_F05.SV.vcf.gz LP6005878-DNA_F06.SV.vcf.gz LP6005878-DNA_F07.SV.vcf.gz LP6005878-DNA_F08.SV.vcf.gz LP6005878-DNA_G01.SV.vcf.gz LP6005878-DNA_G02.SV.vcf.gz LP6005878-DNA_G03.SV.vcf.gz LP6005878-DNA_G04.SV.vcf.gz LP6005878-DNA_G05.SV.vcf.gz LP6005878-DNA_G06.SV.vcf.gz LP6005878-DNA_G07.SV.vcf.gz LP6005878-DNA_G08.SV.vcf.gz LP6005878-DNA_H01.SV.vcf.gz LP6005878-DNA_H02.SV.vcf.gz LP6005878-DNA_H03.SV.vcf.gz LP6005878-DNA_H04.SV.vcf.gz LP6005878-DNA_H05.SV.vcf.gz LP6005878-DNA_H06.SV.vcf.gz LP6005878-DNA_H07.SV.vcf.gz LP6005878-DNA_H08.SV.vcf.gz; Date=Wed Oct 12 04:23:57 2022 -##bcftools_viewVersion=1.7+htslib-1.7-2 -##bcftools_viewCommand=view -R regions merged.vcf.gz; Date=Wed Oct 12 05:38:42 2022 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT LP6005878-DNA_A01 LP6005878-DNA_A02 LP6005878-DNA_A03 LP6005878-DNA_A04 LP6005878-DNA_A05 LP6005878-DNA_A06 LP6005878-DNA_A07 LP6005878-DNA_A08 LP6005878-DNA_A09 LP6005878-DNA_B01 LP6005878-DNA_B02 LP6005878-DNA_B03 LP6005878-DNA_B04 LP6005878-DNA_B05 LP6005878-DNA_B06 LP6005878-DNA_B07 LP6005878-DNA_B08 LP6005878-DNA_B09 LP6005878-DNA_C01 LP6005878-DNA_C02 LP6005878-DNA_C03 LP6005878-DNA_C04 LP6005878-DNA_C05 LP6005878-DNA_C06 LP6005878-DNA_C07 LP6005878-DNA_C08 LP6005878-DNA_C09 LP6005878-DNA_D01 LP6005878-DNA_D02 LP6005878-DNA_D03 LP6005878-DNA_D04 LP6005878-DNA_D05 LP6005878-DNA_D06 LP6005878-DNA_D07 LP6005878-DNA_D08 LP6005878-DNA_E01 LP6005878-DNA_E02 LP6005878-DNA_E03 LP6005878-DNA_E04 LP6005878-DNA_E05 LP6005878-DNA_E06 LP6005878-DNA_E07 LP6005878-DNA_E08 LP6005878-DNA_F01 LP6005878-DNA_F02 LP6005878-DNA_F03 LP6005878-DNA_F04 LP6005878-DNA_F05 LP6005878-DNA_F06 LP6005878-DNA_F07 LP6005878-DNA_F08 LP6005878-DNA_G01 LP6005878-DNA_G02 LP6005878-DNA_G03 LP6005878-DNA_G04 LP6005878-DNA_G05 LP6005878-DNA_G06 LP6005878-DNA_G07 LP6005878-DNA_G08 LP6005878-DNA_H01 LP6005878-DNA_H02 LP6005878-DNA_H03 LP6005878-DNA_H04 LP6005878-DNA_H05 LP6005878-DNA_H06 LP6005878-DNA_H07 LP6005878-DNA_H08 -chr2 202567969 chr2:GROUPER:INS:0:671 C CTGCCCACTCCCAAGGCCCCATCAGTGATTCTAGGGGGCATCCCCCAGGCTGGGGCACTGGAGACCCTCACTCACCAGGGACAGCTTTCCGGACTTCACTGTACACTGTCTCTGTGTCCTTCTTTCCTAGA 4 PASS NS=1;SVTYPE=INS;SVLEN=130;READSOURCES=(0:2);UPSTREAM=TCTTCTTTTCTCT;DOWNSTREAM=.;CONTIG=TCTTCTTTTCTCTGCCCACTCCCAAGGCCCCATCAGTGATTCTAGGGGGCATCCCCCAGGCTGGGGCACTGGAGACCCTCACTCACCAGGGACAGCTTTCCGGACTTCACTGTACACTGTCTCTGTGTCCTTCTTTCCTAGAT;CONTIG_NUM=1082;CLUSTER_NUM=1349;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202580937 chr2:GROUPER:DEL:0:698;chr2:GROUPER:DEL:0:645;chr2:GROUPER:DEL:0:563;chr2:GROUPER:DEL:0:659;chr2:GROUPER:DEL:0:602 CCTGGCCAACATGGTGAAACTCTGTCTCTACTAAAAACACAAAAAATTGGCTGGGCATGGTGGCTCACGCCTGTAATCCTAGCACTTTGGGAGGCCAAAGAGGGTGGATCGCCTGAGGTCAGGAGTTCAAGACCAGCCAGGCCAA C 74 PASS NS=1;SVTYPE=DEL;SVLEN=-144;READSOURCES=(0:2);UPSTREAM=TGGGAGGCTGAGGAAGGTGGAACACCTGAGGTCAGGAGTTCCAGACCAGC;DOWNSTREAM=CATGGAGAAACCCCATCTCTACTAAAAATAC-AAAATTAGCCAGGTGTGGTGGCACATGCCTGTA;CONTIG=TGGGAGGCTGAGGAAGGTGGAACACCTGAGGTCAGGAGTTCCAGACCAGCCATGGAGAAACCCCATCTCTACTAAAAATACAAAATTAGCCAGGTGTGGTGGCACATGCCTGTA;CONTIG_NUM=1157;CLUSTER_NUM=1404;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. 1/. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202581115 chr2:GROUPER:INS:0:715 A AGAAAGAAAAGAAAAGAAAGAACATTGAATCCGTAGACCACTTTTGGTAGTAGTGACATTTTAACAATATTAAGTCTATAACCTCTTGAACAAGAGTGTGTTTGAGAATTTGTT 4 PASS NS=1;SVTYPE=INS;SVLEN=113;READSOURCES=(0:2);UPSTREAM=AAAATACAAA;DOWNSTREAM=.;CONTIG=AAAATACAAAGAAAGAAAAGAAAAGAAAGAACATTGAATCCGTAGACCACTTTTGGTAGTAGTGACATTTTAACAATATTAAGTCTATAACCTCTTGAACAAGAGTGTGTTTGAGAATTTGTT;CONTIG_NUM=1112;CLUSTER_NUM=1395;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202581266 chr2:GROUPER:DEL:0:697 AAAAAAAAAAAAAAAAAAAAAAATTAGCCAGGCGTGGTGGCCCGTACCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGTGCAGGTTGCAGTGAGCTGAGATCACGCCACTGCAGTCCAGCCTGGGTGACAAAGTGAGACTCCATCTC A 38 PASS NS=1;SVTYPE=DEL;SVLEN=-171;READSOURCES=(0:2);UPSTREAM=CTCCATCTCA;DOWNSTREAM=AAAAAAAAAAAAAAATTTAAAAATTAAAAAAAAATAAAAA;CONTIG=CTCCATCTCAAAAAAAAAAAAAAAATTTAAAAATTAAAAAAAAATAAAAA;CONTIG_NUM=1120;CLUSTER_NUM=1400;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202581288 chr2:GROUPER:INS:0:644;chr2:GROUPER:INS:0:743;chr2:GROUPER:INS:0:727 A AAGAAAGAACATTGAATCCGTAGACCACTTTTGGTAGTAGTGACATTTTAACAATATTAAGTCTATAACCT,AGAACATTGAATCCGTAGACCACTTTTGGTAGTAGTGACATTTTAACAATATTAAGTC,AAGAAAGAACATTGAATCCGTAGACCACTTTTGGTAGTAGTGACATTTTAACAATATTAAGTCTATAACCTCTTGAACAAGAGTGTGTTTGAGAATTTGTTGTTTAATTTTTACTTATTCT 9 PASS NS=1;SVTYPE=INS;SVLEN=70;READSOURCES=(0:2);UPSTREAM=TCTCAAAATAAAAAGAAAGAAAAGAAA;DOWNSTREAM=.;CONTIG=TCTCAAAATAAAAAGAAAGAAAAGAAAAGAAAGAACATTGAATCCGTAGACCACTTTTGGTAGTAGTGACATTTTAACAATATTAAGTCTATAACCT;CONTIG_NUM=1052;CLUSTER_NUM=1416;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 3/. ./. -chr2 202581590 chr2:GROUPER:INS:0:675 A AGTGTTTTTAACTTCTTGTTTTATTGTATCATAGTTAGGAATAATTTGTGTAATTCCATCTGCTGAAATTTGCTAAGATGTGTTTTTTAACTTAACAGGTGGTCTATCTGGAATATTGTGGCATGTGTGATTAAAAGTATTGCAT 2 PASS NS=1;SVTYPE=INS;SVLEN=144;READSOURCES=(0:4);UPSTREAM=ACATGGTA;DOWNSTREAM=.;CONTIG=ACATGGTAGTGTTTTTAACTTCTTGTTTTATTGTATCATAGTTAGGAATAATTTGTGTAATTCCATCTGCTGAAATTTGCTAAGATGTGTTTTTTAACTTAACAGGTGGTCTATCTGGAATATTGTGGCATGTGTGATTAAAAGTATTGCAT;CONTIG_NUM=923;CLUSTER_NUM=904;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202607809 chr2:GROUPER:DEL:0:669;chr2:GROUPER:DEL:0:668;chr2:GROUPER:DEL:0:661;chr2:GROUPER:DEL:0:702;chr2:GROUPER:DEL:0:755 AGAAAGAAACAATGGGCTGACCTGCAGAAGACAATGTCCTCAACATGGCAAAAGTGATGTACTAGAGAATTAACCTGAATTCTGGGTCAACACAGTGGGGCAAGGAGTGCAGGAGAGAGAAAG A 82 PASS NS=1;SVTYPE=DEL;SVLEN=-122;READSOURCES=(0:2);UPSTREAM=CCGAGATTGTGCCACTACACTCCAGCCTGGGTGACAGAGCAAGACTCTGTCTCAAAAAAAAAAAAAAAA;DOWNSTREAM=AGAAAGAAA;CONTIG=CCGAGATTGTGCCACTACACTCCAGCCTGGGTGACAGAGCAAGACTCTGTCTCAAAAAAAAAAAAAAAAAGAAAGAAA;CONTIG_NUM=1070;CLUSTER_NUM=1338;ensembl_gene_id=ENSG00000003393 GT ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202631459 chr2:GROUPER:INS:0:702;chr2:GROUPER:INS:0:673;chr2:GROUPER:INS:0:755 t tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGAGCCACCGGTGAGGAGAATGACAACAACCCCGCTAAAAAGGTG,tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTG,tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAA 68 PASS NS=1;SVTYPE=INS;SVLEN=103;READSOURCES=(0:2);UPSTREAM=ACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATA;DOWNSTREAM=.;CONTIG=ACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGAGCCACCGGTGAGGAGAATGACAACAACCCCGCTAAAAAGGTGA;CONTIG_NUM=1128;CLUSTER_NUM=1407;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. 3/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202631460 chr2:GROUPER:INS:0:659;chr2:GROUPER:INS:0:714;chr2:GROUPER:INS:0:673;chr2:GROUPER:INS:0:588;chr2:GROUPER:INS:0:811;chr2:GROUPER:INS:0:701;chr2:GROUPER:INS:0:744;chr2:GROUPER:INS:0:703;chr2:GROUPER:INS:0:721;chr2:GROUPER:INS:0:620;chr2:GROUPER:INS:0:718;chr2:GROUPER:INS:0:764;chr2:GROUPER:INS:0:666;chr2:GROUPER:INS:0:693;chr2:GROUPER:INS:0:514;chr2:GROUPER:INS:0:789 A AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCT,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGC,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCG 74 PASS NS=1;SVTYPE=INS;SVLEN=115;READSOURCES=(0:8);UPSTREAM=AAAAGCAAAGACTTGGAACCAACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATA;DOWNSTREAM=.;CONTIG=AAAAGCAAAGACTTGGAACCAACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCT;CONTIG_NUM=842;CLUSTER_NUM=838;ensembl_gene_id=ENSG00000003393 GT 1/. ./. ./. ./. ./. ./. 2/. ./. 3/. ./. ./. ./. ./. ./. 4/. ./. ./. 5/. ./. ./. ./. ./. 6/. ./. ./. 5/. ./. ./. ./. ./. 2/. ./. 2/. ./. ./. 7/. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. 2/. ./. ./. 8/. ./. ./. ./. ./. ./. ./. ./. 9/. 10/. 11/. 12/. ./. ./. ./. 6/. -chr2 202567969 chr2:GROUPER:INS:0:671 C CTGCCCACTCCCAAGGCCCCATCAGTGATTCTAGGGGGCATCCCCCAGGCTGGGGCACTGGAGACCCTCACTCACCAGGGACAGCTTTCCGGACTTCACTGTACACTGTCTCTGTGTCCTTCTTTCCTAGA 4 PASS NS=1;SVTYPE=INS;SVLEN=130;READSOURCES=(0:2);UPSTREAM=TCTTCTTTTCTCT;DOWNSTREAM=.;CONTIG=TCTTCTTTTCTCTGCCCACTCCCAAGGCCCCATCAGTGATTCTAGGGGGCATCCCCCAGGCTGGGGCACTGGAGACCCTCACTCACCAGGGACAGCTTTCCGGACTTCACTGTACACTGTCTCTGTGTCCTTCTTTCCTAGAT;CONTIG_NUM=1082;CLUSTER_NUM=1349;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202580937 chr2:GROUPER:DEL:0:698;chr2:GROUPER:DEL:0:645;chr2:GROUPER:DEL:0:563;chr2:GROUPER:DEL:0:659;chr2:GROUPER:DEL:0:602 CCTGGCCAACATGGTGAAACTCTGTCTCTACTAAAAACACAAAAAATTGGCTGGGCATGGTGGCTCACGCCTGTAATCCTAGCACTTTGGGAGGCCAAAGAGGGTGGATCGCCTGAGGTCAGGAGTTCAAGACCAGCCAGGCCAA C 74 PASS NS=1;SVTYPE=DEL;SVLEN=-144;READSOURCES=(0:2);UPSTREAM=TGGGAGGCTGAGGAAGGTGGAACACCTGAGGTCAGGAGTTCCAGACCAGC;DOWNSTREAM=CATGGAGAAACCCCATCTCTACTAAAAATAC-AAAATTAGCCAGGTGTGGTGGCACATGCCTGTA;CONTIG=TGGGAGGCTGAGGAAGGTGGAACACCTGAGGTCAGGAGTTCCAGACCAGCCATGGAGAAACCCCATCTCTACTAAAAATACAAAATTAGCCAGGTGTGGTGGCACATGCCTGTA;CONTIG_NUM=1157;CLUSTER_NUM=1404;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. 1/. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202581115 chr2:GROUPER:INS:0:715 A AGAAAGAAAAGAAAAGAAAGAACATTGAATCCGTAGACCACTTTTGGTAGTAGTGACATTTTAACAATATTAAGTCTATAACCTCTTGAACAAGAGTGTGTTTGAGAATTTGTT 4 PASS NS=1;SVTYPE=INS;SVLEN=113;READSOURCES=(0:2);UPSTREAM=AAAATACAAA;DOWNSTREAM=.;CONTIG=AAAATACAAAGAAAGAAAAGAAAAGAAAGAACATTGAATCCGTAGACCACTTTTGGTAGTAGTGACATTTTAACAATATTAAGTCTATAACCTCTTGAACAAGAGTGTGTTTGAGAATTTGTT;CONTIG_NUM=1112;CLUSTER_NUM=1395;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202581266 chr2:GROUPER:DEL:0:697 AAAAAAAAAAAAAAAAAAAAAAATTAGCCAGGCGTGGTGGCCCGTACCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGTGCAGGTTGCAGTGAGCTGAGATCACGCCACTGCAGTCCAGCCTGGGTGACAAAGTGAGACTCCATCTC A 38 PASS NS=1;SVTYPE=DEL;SVLEN=-171;READSOURCES=(0:2);UPSTREAM=CTCCATCTCA;DOWNSTREAM=AAAAAAAAAAAAAAATTTAAAAATTAAAAAAAAATAAAAA;CONTIG=CTCCATCTCAAAAAAAAAAAAAAAATTTAAAAATTAAAAAAAAATAAAAA;CONTIG_NUM=1120;CLUSTER_NUM=1400;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202581288 chr2:GROUPER:INS:0:644;chr2:GROUPER:INS:0:743;chr2:GROUPER:INS:0:727 A AAGAAAGAACATTGAATCCGTAGACCACTTTTGGTAGTAGTGACATTTTAACAATATTAAGTCTATAACCT,AGAACATTGAATCCGTAGACCACTTTTGGTAGTAGTGACATTTTAACAATATTAAGTC,AAGAAAGAACATTGAATCCGTAGACCACTTTTGGTAGTAGTGACATTTTAACAATATTAAGTCTATAACCTCTTGAACAAGAGTGTGTTTGAGAATTTGTTGTTTAATTTTTACTTATTCT 9 PASS NS=1;SVTYPE=INS;SVLEN=70;READSOURCES=(0:2);UPSTREAM=TCTCAAAATAAAAAGAAAGAAAAGAAA;DOWNSTREAM=.;CONTIG=TCTCAAAATAAAAAGAAAGAAAAGAAAAGAAAGAACATTGAATCCGTAGACCACTTTTGGTAGTAGTGACATTTTAACAATATTAAGTCTATAACCT;CONTIG_NUM=1052;CLUSTER_NUM=1416;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 3/. ./. -chr2 202581590 chr2:GROUPER:INS:0:675 A AGTGTTTTTAACTTCTTGTTTTATTGTATCATAGTTAGGAATAATTTGTGTAATTCCATCTGCTGAAATTTGCTAAGATGTGTTTTTTAACTTAACAGGTGGTCTATCTGGAATATTGTGGCATGTGTGATTAAAAGTATTGCAT 2 PASS NS=1;SVTYPE=INS;SVLEN=144;READSOURCES=(0:4);UPSTREAM=ACATGGTA;DOWNSTREAM=.;CONTIG=ACATGGTAGTGTTTTTAACTTCTTGTTTTATTGTATCATAGTTAGGAATAATTTGTGTAATTCCATCTGCTGAAATTTGCTAAGATGTGTTTTTTAACTTAACAGGTGGTCTATCTGGAATATTGTGGCATGTGTGATTAAAAGTATTGCAT;CONTIG_NUM=923;CLUSTER_NUM=904;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202607809 chr2:GROUPER:DEL:0:669;chr2:GROUPER:DEL:0:668;chr2:GROUPER:DEL:0:661;chr2:GROUPER:DEL:0:702;chr2:GROUPER:DEL:0:755 AGAAAGAAACAATGGGCTGACCTGCAGAAGACAATGTCCTCAACATGGCAAAAGTGATGTACTAGAGAATTAACCTGAATTCTGGGTCAACACAGTGGGGCAAGGAGTGCAGGAGAGAGAAAG A 82 PASS NS=1;SVTYPE=DEL;SVLEN=-122;READSOURCES=(0:2);UPSTREAM=CCGAGATTGTGCCACTACACTCCAGCCTGGGTGACAGAGCAAGACTCTGTCTCAAAAAAAAAAAAAAAA;DOWNSTREAM=AGAAAGAAA;CONTIG=CCGAGATTGTGCCACTACACTCCAGCCTGGGTGACAGAGCAAGACTCTGTCTCAAAAAAAAAAAAAAAAAGAAAGAAA;CONTIG_NUM=1070;CLUSTER_NUM=1338;ensembl_gene_id=ENSG00000003393 GT ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202581266 chr2:GROUPER:DEL:0:697 AAAAAAAAAAAAAAAAAAAAAAATTAGCCAGGCGTGGTGGCCCGTACCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGTGCAGGTTGCAGTGAGCTGAGATCACGCCACTGCAGTCCAGCCTGGGTGACAAAGTGAGACTCCATCTC A 38 PASS NS=1;SVTYPE=DEL;SVLEN=-171;READSOURCES=(0:2);UPSTREAM=CTCCATCTCA;DOWNSTREAM=AAAAAAAAAAAAAAATTTAAAAATTAAAAAAAAATAAAAA;CONTIG=CTCCATCTCAAAAAAAAAAAAAAAATTTAAAAATTAAAAAAAAATAAAAA;CONTIG_NUM=1120;CLUSTER_NUM=1400;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202581590 chr2:GROUPER:INS:0:675 A AGTGTTTTTAACTTCTTGTTTTATTGTATCATAGTTAGGAATAATTTGTGTAATTCCATCTGCTGAAATTTGCTAAGATGTGTTTTTTAACTTAACAGGTGGTCTATCTGGAATATTGTGGCATGTGTGATTAAAAGTATTGCAT 2 PASS NS=1;SVTYPE=INS;SVLEN=144;READSOURCES=(0:4);UPSTREAM=ACATGGTA;DOWNSTREAM=.;CONTIG=ACATGGTAGTGTTTTTAACTTCTTGTTTTATTGTATCATAGTTAGGAATAATTTGTGTAATTCCATCTGCTGAAATTTGCTAAGATGTGTTTTTTAACTTAACAGGTGGTCTATCTGGAATATTGTGGCATGTGTGATTAAAAGTATTGCAT;CONTIG_NUM=923;CLUSTER_NUM=904;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202581266 chr2:GROUPER:DEL:0:697 AAAAAAAAAAAAAAAAAAAAAAATTAGCCAGGCGTGGTGGCCCGTACCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGTGCAGGTTGCAGTGAGCTGAGATCACGCCACTGCAGTCCAGCCTGGGTGACAAAGTGAGACTCCATCTC A 38 PASS NS=1;SVTYPE=DEL;SVLEN=-171;READSOURCES=(0:2);UPSTREAM=CTCCATCTCA;DOWNSTREAM=AAAAAAAAAAAAAAATTTAAAAATTAAAAAAAAATAAAAA;CONTIG=CTCCATCTCAAAAAAAAAAAAAAAATTTAAAAATTAAAAAAAAATAAAAA;CONTIG_NUM=1120;CLUSTER_NUM=1400;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202567969 chr2:GROUPER:INS:0:671 C CTGCCCACTCCCAAGGCCCCATCAGTGATTCTAGGGGGCATCCCCCAGGCTGGGGCACTGGAGACCCTCACTCACCAGGGACAGCTTTCCGGACTTCACTGTACACTGTCTCTGTGTCCTTCTTTCCTAGA 4 PASS NS=1;SVTYPE=INS;SVLEN=130;READSOURCES=(0:2);UPSTREAM=TCTTCTTTTCTCT;DOWNSTREAM=.;CONTIG=TCTTCTTTTCTCTGCCCACTCCCAAGGCCCCATCAGTGATTCTAGGGGGCATCCCCCAGGCTGGGGCACTGGAGACCCTCACTCACCAGGGACAGCTTTCCGGACTTCACTGTACACTGTCTCTGTGTCCTTCTTTCCTAGAT;CONTIG_NUM=1082;CLUSTER_NUM=1349;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202580937 chr2:GROUPER:DEL:0:698;chr2:GROUPER:DEL:0:645;chr2:GROUPER:DEL:0:563;chr2:GROUPER:DEL:0:659;chr2:GROUPER:DEL:0:602 CCTGGCCAACATGGTGAAACTCTGTCTCTACTAAAAACACAAAAAATTGGCTGGGCATGGTGGCTCACGCCTGTAATCCTAGCACTTTGGGAGGCCAAAGAGGGTGGATCGCCTGAGGTCAGGAGTTCAAGACCAGCCAGGCCAA C 74 PASS NS=1;SVTYPE=DEL;SVLEN=-144;READSOURCES=(0:2);UPSTREAM=TGGGAGGCTGAGGAAGGTGGAACACCTGAGGTCAGGAGTTCCAGACCAGC;DOWNSTREAM=CATGGAGAAACCCCATCTCTACTAAAAATAC-AAAATTAGCCAGGTGTGGTGGCACATGCCTGTA;CONTIG=TGGGAGGCTGAGGAAGGTGGAACACCTGAGGTCAGGAGTTCCAGACCAGCCATGGAGAAACCCCATCTCTACTAAAAATACAAAATTAGCCAGGTGTGGTGGCACATGCCTGTA;CONTIG_NUM=1157;CLUSTER_NUM=1404;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. 1/. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202581115 chr2:GROUPER:INS:0:715 A AGAAAGAAAAGAAAAGAAAGAACATTGAATCCGTAGACCACTTTTGGTAGTAGTGACATTTTAACAATATTAAGTCTATAACCTCTTGAACAAGAGTGTGTTTGAGAATTTGTT 4 PASS NS=1;SVTYPE=INS;SVLEN=113;READSOURCES=(0:2);UPSTREAM=AAAATACAAA;DOWNSTREAM=.;CONTIG=AAAATACAAAGAAAGAAAAGAAAAGAAAGAACATTGAATCCGTAGACCACTTTTGGTAGTAGTGACATTTTAACAATATTAAGTCTATAACCTCTTGAACAAGAGTGTGTTTGAGAATTTGTT;CONTIG_NUM=1112;CLUSTER_NUM=1395;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202581266 chr2:GROUPER:DEL:0:697 AAAAAAAAAAAAAAAAAAAAAAATTAGCCAGGCGTGGTGGCCCGTACCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGTGCAGGTTGCAGTGAGCTGAGATCACGCCACTGCAGTCCAGCCTGGGTGACAAAGTGAGACTCCATCTC A 38 PASS NS=1;SVTYPE=DEL;SVLEN=-171;READSOURCES=(0:2);UPSTREAM=CTCCATCTCA;DOWNSTREAM=AAAAAAAAAAAAAAATTTAAAAATTAAAAAAAAATAAAAA;CONTIG=CTCCATCTCAAAAAAAAAAAAAAAATTTAAAAATTAAAAAAAAATAAAAA;CONTIG_NUM=1120;CLUSTER_NUM=1400;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202581288 chr2:GROUPER:INS:0:644;chr2:GROUPER:INS:0:743;chr2:GROUPER:INS:0:727 A AAGAAAGAACATTGAATCCGTAGACCACTTTTGGTAGTAGTGACATTTTAACAATATTAAGTCTATAACCT,AGAACATTGAATCCGTAGACCACTTTTGGTAGTAGTGACATTTTAACAATATTAAGTC,AAGAAAGAACATTGAATCCGTAGACCACTTTTGGTAGTAGTGACATTTTAACAATATTAAGTCTATAACCTCTTGAACAAGAGTGTGTTTGAGAATTTGTTGTTTAATTTTTACTTATTCT 9 PASS NS=1;SVTYPE=INS;SVLEN=70;READSOURCES=(0:2);UPSTREAM=TCTCAAAATAAAAAGAAAGAAAAGAAA;DOWNSTREAM=.;CONTIG=TCTCAAAATAAAAAGAAAGAAAAGAAAAGAAAGAACATTGAATCCGTAGACCACTTTTGGTAGTAGTGACATTTTAACAATATTAAGTCTATAACCT;CONTIG_NUM=1052;CLUSTER_NUM=1416;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 3/. ./. -chr2 202581590 chr2:GROUPER:INS:0:675 A AGTGTTTTTAACTTCTTGTTTTATTGTATCATAGTTAGGAATAATTTGTGTAATTCCATCTGCTGAAATTTGCTAAGATGTGTTTTTTAACTTAACAGGTGGTCTATCTGGAATATTGTGGCATGTGTGATTAAAAGTATTGCAT 2 PASS NS=1;SVTYPE=INS;SVLEN=144;READSOURCES=(0:4);UPSTREAM=ACATGGTA;DOWNSTREAM=.;CONTIG=ACATGGTAGTGTTTTTAACTTCTTGTTTTATTGTATCATAGTTAGGAATAATTTGTGTAATTCCATCTGCTGAAATTTGCTAAGATGTGTTTTTTAACTTAACAGGTGGTCTATCTGGAATATTGTGGCATGTGTGATTAAAAGTATTGCAT;CONTIG_NUM=923;CLUSTER_NUM=904;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202607809 chr2:GROUPER:DEL:0:669;chr2:GROUPER:DEL:0:668;chr2:GROUPER:DEL:0:661;chr2:GROUPER:DEL:0:702;chr2:GROUPER:DEL:0:755 AGAAAGAAACAATGGGCTGACCTGCAGAAGACAATGTCCTCAACATGGCAAAAGTGATGTACTAGAGAATTAACCTGAATTCTGGGTCAACACAGTGGGGCAAGGAGTGCAGGAGAGAGAAAG A 82 PASS NS=1;SVTYPE=DEL;SVLEN=-122;READSOURCES=(0:2);UPSTREAM=CCGAGATTGTGCCACTACACTCCAGCCTGGGTGACAGAGCAAGACTCTGTCTCAAAAAAAAAAAAAAAA;DOWNSTREAM=AGAAAGAAA;CONTIG=CCGAGATTGTGCCACTACACTCCAGCCTGGGTGACAGAGCAAGACTCTGTCTCAAAAAAAAAAAAAAAAAGAAAGAAA;CONTIG_NUM=1070;CLUSTER_NUM=1338;ensembl_gene_id=ENSG00000003393 GT ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202607809 chr2:GROUPER:DEL:0:669;chr2:GROUPER:DEL:0:668;chr2:GROUPER:DEL:0:661;chr2:GROUPER:DEL:0:702;chr2:GROUPER:DEL:0:755 AGAAAGAAACAATGGGCTGACCTGCAGAAGACAATGTCCTCAACATGGCAAAAGTGATGTACTAGAGAATTAACCTGAATTCTGGGTCAACACAGTGGGGCAAGGAGTGCAGGAGAGAGAAAG A 82 PASS NS=1;SVTYPE=DEL;SVLEN=-122;READSOURCES=(0:2);UPSTREAM=CCGAGATTGTGCCACTACACTCCAGCCTGGGTGACAGAGCAAGACTCTGTCTCAAAAAAAAAAAAAAAA;DOWNSTREAM=AGAAAGAAA;CONTIG=CCGAGATTGTGCCACTACACTCCAGCCTGGGTGACAGAGCAAGACTCTGTCTCAAAAAAAAAAAAAAAAAGAAAGAAA;CONTIG_NUM=1070;CLUSTER_NUM=1338;ensembl_gene_id=ENSG00000003393 GT ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202631459 chr2:GROUPER:INS:0:702;chr2:GROUPER:INS:0:673;chr2:GROUPER:INS:0:755 t tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGAGCCACCGGTGAGGAGAATGACAACAACCCCGCTAAAAAGGTG,tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTG,tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAA 68 PASS NS=1;SVTYPE=INS;SVLEN=103;READSOURCES=(0:2);UPSTREAM=ACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATA;DOWNSTREAM=.;CONTIG=ACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGAGCCACCGGTGAGGAGAATGACAACAACCCCGCTAAAAAGGTGA;CONTIG_NUM=1128;CLUSTER_NUM=1407;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. 3/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202631460 chr2:GROUPER:INS:0:659;chr2:GROUPER:INS:0:714;chr2:GROUPER:INS:0:673;chr2:GROUPER:INS:0:588;chr2:GROUPER:INS:0:811;chr2:GROUPER:INS:0:701;chr2:GROUPER:INS:0:744;chr2:GROUPER:INS:0:703;chr2:GROUPER:INS:0:721;chr2:GROUPER:INS:0:620;chr2:GROUPER:INS:0:718;chr2:GROUPER:INS:0:764;chr2:GROUPER:INS:0:666;chr2:GROUPER:INS:0:693;chr2:GROUPER:INS:0:514;chr2:GROUPER:INS:0:789 A AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCT,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGC,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCG 74 PASS NS=1;SVTYPE=INS;SVLEN=115;READSOURCES=(0:8);UPSTREAM=AAAAGCAAAGACTTGGAACCAACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATA;DOWNSTREAM=.;CONTIG=AAAAGCAAAGACTTGGAACCAACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCT;CONTIG_NUM=842;CLUSTER_NUM=838;ensembl_gene_id=ENSG00000003393 GT 1/. ./. ./. ./. ./. ./. 2/. ./. 3/. ./. ./. ./. ./. ./. 4/. ./. ./. 5/. ./. ./. ./. ./. 6/. ./. ./. 5/. ./. ./. ./. ./. 2/. ./. 2/. ./. ./. 7/. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. 2/. ./. ./. 8/. ./. ./. ./. ./. ./. ./. ./. 9/. 10/. 11/. 12/. ./. ./. ./. 6/. -chr2 202607809 chr2:GROUPER:DEL:0:669;chr2:GROUPER:DEL:0:668;chr2:GROUPER:DEL:0:661;chr2:GROUPER:DEL:0:702;chr2:GROUPER:DEL:0:755 AGAAAGAAACAATGGGCTGACCTGCAGAAGACAATGTCCTCAACATGGCAAAAGTGATGTACTAGAGAATTAACCTGAATTCTGGGTCAACACAGTGGGGCAAGGAGTGCAGGAGAGAGAAAG A 82 PASS NS=1;SVTYPE=DEL;SVLEN=-122;READSOURCES=(0:2);UPSTREAM=CCGAGATTGTGCCACTACACTCCAGCCTGGGTGACAGAGCAAGACTCTGTCTCAAAAAAAAAAAAAAAA;DOWNSTREAM=AGAAAGAAA;CONTIG=CCGAGATTGTGCCACTACACTCCAGCCTGGGTGACAGAGCAAGACTCTGTCTCAAAAAAAAAAAAAAAAAGAAAGAAA;CONTIG_NUM=1070;CLUSTER_NUM=1338;ensembl_gene_id=ENSG00000003393 GT ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202631459 chr2:GROUPER:INS:0:702;chr2:GROUPER:INS:0:673;chr2:GROUPER:INS:0:755 t tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGAGCCACCGGTGAGGAGAATGACAACAACCCCGCTAAAAAGGTG,tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTG,tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAA 68 PASS NS=1;SVTYPE=INS;SVLEN=103;READSOURCES=(0:2);UPSTREAM=ACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATA;DOWNSTREAM=.;CONTIG=ACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGAGCCACCGGTGAGGAGAATGACAACAACCCCGCTAAAAAGGTGA;CONTIG_NUM=1128;CLUSTER_NUM=1407;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. 3/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202631460 chr2:GROUPER:INS:0:659;chr2:GROUPER:INS:0:714;chr2:GROUPER:INS:0:673;chr2:GROUPER:INS:0:588;chr2:GROUPER:INS:0:811;chr2:GROUPER:INS:0:701;chr2:GROUPER:INS:0:744;chr2:GROUPER:INS:0:703;chr2:GROUPER:INS:0:721;chr2:GROUPER:INS:0:620;chr2:GROUPER:INS:0:718;chr2:GROUPER:INS:0:764;chr2:GROUPER:INS:0:666;chr2:GROUPER:INS:0:693;chr2:GROUPER:INS:0:514;chr2:GROUPER:INS:0:789 A AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCT,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGC,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCG 74 PASS NS=1;SVTYPE=INS;SVLEN=115;READSOURCES=(0:8);UPSTREAM=AAAAGCAAAGACTTGGAACCAACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATA;DOWNSTREAM=.;CONTIG=AAAAGCAAAGACTTGGAACCAACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCT;CONTIG_NUM=842;CLUSTER_NUM=838;ensembl_gene_id=ENSG00000003393 GT 1/. ./. ./. ./. ./. ./. 2/. ./. 3/. ./. ./. ./. ./. ./. 4/. ./. ./. 5/. ./. ./. ./. ./. 6/. ./. ./. 5/. ./. ./. ./. ./. 2/. ./. 2/. ./. ./. 7/. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. 2/. ./. ./. 8/. ./. ./. ./. ./. ./. ./. ./. 9/. 10/. 11/. 12/. ./. ./. ./. 6/. -chr2 202631459 chr2:GROUPER:INS:0:702;chr2:GROUPER:INS:0:673;chr2:GROUPER:INS:0:755 t tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGAGCCACCGGTGAGGAGAATGACAACAACCCCGCTAAAAAGGTG,tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTG,tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAA 68 PASS NS=1;SVTYPE=INS;SVLEN=103;READSOURCES=(0:2);UPSTREAM=ACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATA;DOWNSTREAM=.;CONTIG=ACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGAGCCACCGGTGAGGAGAATGACAACAACCCCGCTAAAAAGGTGA;CONTIG_NUM=1128;CLUSTER_NUM=1407;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. 3/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202631460 chr2:GROUPER:INS:0:659;chr2:GROUPER:INS:0:714;chr2:GROUPER:INS:0:673;chr2:GROUPER:INS:0:588;chr2:GROUPER:INS:0:811;chr2:GROUPER:INS:0:701;chr2:GROUPER:INS:0:744;chr2:GROUPER:INS:0:703;chr2:GROUPER:INS:0:721;chr2:GROUPER:INS:0:620;chr2:GROUPER:INS:0:718;chr2:GROUPER:INS:0:764;chr2:GROUPER:INS:0:666;chr2:GROUPER:INS:0:693;chr2:GROUPER:INS:0:514;chr2:GROUPER:INS:0:789 A AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCT,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGC,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCG 74 PASS NS=1;SVTYPE=INS;SVLEN=115;READSOURCES=(0:8);UPSTREAM=AAAAGCAAAGACTTGGAACCAACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATA;DOWNSTREAM=.;CONTIG=AAAAGCAAAGACTTGGAACCAACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCT;CONTIG_NUM=842;CLUSTER_NUM=838;ensembl_gene_id=ENSG00000003393 GT 1/. ./. ./. ./. ./. ./. 2/. ./. 3/. ./. ./. ./. ./. ./. 4/. ./. ./. 5/. ./. ./. ./. ./. 6/. ./. ./. 5/. ./. ./. ./. ./. 2/. ./. 2/. ./. ./. 7/. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. 2/. ./. ./. 8/. ./. ./. ./. ./. ./. ./. ./. 9/. 10/. 11/. 12/. ./. ./. ./. 6/. -chr2 202631459 chr2:GROUPER:INS:0:702;chr2:GROUPER:INS:0:673;chr2:GROUPER:INS:0:755 t tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGAGCCACCGGTGAGGAGAATGACAACAACCCCGCTAAAAAGGTG,tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTG,tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAA 68 PASS NS=1;SVTYPE=INS;SVLEN=103;READSOURCES=(0:2);UPSTREAM=ACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATA;DOWNSTREAM=.;CONTIG=ACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGAGCCACCGGTGAGGAGAATGACAACAACCCCGCTAAAAAGGTGA;CONTIG_NUM=1128;CLUSTER_NUM=1407;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. 3/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202631460 chr2:GROUPER:INS:0:659;chr2:GROUPER:INS:0:714;chr2:GROUPER:INS:0:673;chr2:GROUPER:INS:0:588;chr2:GROUPER:INS:0:811;chr2:GROUPER:INS:0:701;chr2:GROUPER:INS:0:744;chr2:GROUPER:INS:0:703;chr2:GROUPER:INS:0:721;chr2:GROUPER:INS:0:620;chr2:GROUPER:INS:0:718;chr2:GROUPER:INS:0:764;chr2:GROUPER:INS:0:666;chr2:GROUPER:INS:0:693;chr2:GROUPER:INS:0:514;chr2:GROUPER:INS:0:789 A AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCT,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGC,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCG 74 PASS NS=1;SVTYPE=INS;SVLEN=115;READSOURCES=(0:8);UPSTREAM=AAAAGCAAAGACTTGGAACCAACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATA;DOWNSTREAM=.;CONTIG=AAAAGCAAAGACTTGGAACCAACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCT;CONTIG_NUM=842;CLUSTER_NUM=838;ensembl_gene_id=ENSG00000003393 GT 1/. ./. ./. ./. ./. ./. 2/. ./. 3/. ./. ./. ./. ./. ./. 4/. ./. ./. 5/. ./. ./. ./. ./. 6/. ./. ./. 5/. ./. ./. ./. ./. 2/. ./. 2/. ./. ./. 7/. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. 2/. ./. ./. 8/. ./. ./. ./. ./. ./. ./. ./. 9/. 10/. 11/. 12/. ./. ./. ./. 6/. -chr2 202631459 chr2:GROUPER:INS:0:702;chr2:GROUPER:INS:0:673;chr2:GROUPER:INS:0:755 t tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGAGCCACCGGTGAGGAGAATGACAACAACCCCGCTAAAAAGGTG,tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTG,tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAA 68 PASS NS=1;SVTYPE=INS;SVLEN=103;READSOURCES=(0:2);UPSTREAM=ACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATA;DOWNSTREAM=.;CONTIG=ACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGAGCCACCGGTGAGGAGAATGACAACAACCCCGCTAAAAAGGTGA;CONTIG_NUM=1128;CLUSTER_NUM=1407;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. 3/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202631460 chr2:GROUPER:INS:0:659;chr2:GROUPER:INS:0:714;chr2:GROUPER:INS:0:673;chr2:GROUPER:INS:0:588;chr2:GROUPER:INS:0:811;chr2:GROUPER:INS:0:701;chr2:GROUPER:INS:0:744;chr2:GROUPER:INS:0:703;chr2:GROUPER:INS:0:721;chr2:GROUPER:INS:0:620;chr2:GROUPER:INS:0:718;chr2:GROUPER:INS:0:764;chr2:GROUPER:INS:0:666;chr2:GROUPER:INS:0:693;chr2:GROUPER:INS:0:514;chr2:GROUPER:INS:0:789 A AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCT,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGC,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCG 74 PASS NS=1;SVTYPE=INS;SVLEN=115;READSOURCES=(0:8);UPSTREAM=AAAAGCAAAGACTTGGAACCAACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATA;DOWNSTREAM=.;CONTIG=AAAAGCAAAGACTTGGAACCAACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCT;CONTIG_NUM=842;CLUSTER_NUM=838;ensembl_gene_id=ENSG00000003393 GT 1/. ./. ./. ./. ./. ./. 2/. ./. 3/. ./. ./. ./. ./. ./. 4/. ./. ./. 5/. ./. ./. ./. ./. 6/. ./. ./. 5/. ./. ./. ./. ./. 2/. ./. 2/. ./. ./. 7/. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. 2/. ./. ./. 8/. ./. ./. ./. ./. ./. ./. ./. 9/. 10/. 11/. 12/. ./. ./. ./. 6/. -chr2 202631459 chr2:GROUPER:INS:0:702;chr2:GROUPER:INS:0:673;chr2:GROUPER:INS:0:755 t tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGAGCCACCGGTGAGGAGAATGACAACAACCCCGCTAAAAAGGTG,tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTG,tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAA 68 PASS NS=1;SVTYPE=INS;SVLEN=103;READSOURCES=(0:2);UPSTREAM=ACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATA;DOWNSTREAM=.;CONTIG=ACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGAGCCACCGGTGAGGAGAATGACAACAACCCCGCTAAAAAGGTGA;CONTIG_NUM=1128;CLUSTER_NUM=1407;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. 3/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202631460 chr2:GROUPER:INS:0:659;chr2:GROUPER:INS:0:714;chr2:GROUPER:INS:0:673;chr2:GROUPER:INS:0:588;chr2:GROUPER:INS:0:811;chr2:GROUPER:INS:0:701;chr2:GROUPER:INS:0:744;chr2:GROUPER:INS:0:703;chr2:GROUPER:INS:0:721;chr2:GROUPER:INS:0:620;chr2:GROUPER:INS:0:718;chr2:GROUPER:INS:0:764;chr2:GROUPER:INS:0:666;chr2:GROUPER:INS:0:693;chr2:GROUPER:INS:0:514;chr2:GROUPER:INS:0:789 A AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCT,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGC,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCG 74 PASS NS=1;SVTYPE=INS;SVLEN=115;READSOURCES=(0:8);UPSTREAM=AAAAGCAAAGACTTGGAACCAACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATA;DOWNSTREAM=.;CONTIG=AAAAGCAAAGACTTGGAACCAACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCT;CONTIG_NUM=842;CLUSTER_NUM=838;ensembl_gene_id=ENSG00000003393 GT 1/. ./. ./. ./. ./. ./. 2/. ./. 3/. ./. ./. ./. ./. ./. 4/. ./. ./. 5/. ./. ./. ./. ./. 6/. ./. ./. 5/. ./. ./. ./. ./. 2/. ./. 2/. ./. ./. 7/. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. 2/. ./. ./. 8/. ./. ./. ./. ./. ./. ./. ./. 9/. 10/. 11/. 12/. ./. ./. ./. 6/. -chr2 202631459 chr2:GROUPER:INS:0:702;chr2:GROUPER:INS:0:673;chr2:GROUPER:INS:0:755 t tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGAGCCACCGGTGAGGAGAATGACAACAACCCCGCTAAAAAGGTG,tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTG,tAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAA 68 PASS NS=1;SVTYPE=INS;SVLEN=103;READSOURCES=(0:2);UPSTREAM=ACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATA;DOWNSTREAM=.;CONTIG=ACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGAGCCACCGGTGAGGAGAATGACAACAACCCCGCTAAAAAGGTGA;CONTIG_NUM=1128;CLUSTER_NUM=1407;ensembl_gene_id=ENSG00000003393 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. 3/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr2 202631460 chr2:GROUPER:INS:0:659;chr2:GROUPER:INS:0:714;chr2:GROUPER:INS:0:673;chr2:GROUPER:INS:0:588;chr2:GROUPER:INS:0:811;chr2:GROUPER:INS:0:701;chr2:GROUPER:INS:0:744;chr2:GROUPER:INS:0:703;chr2:GROUPER:INS:0:721;chr2:GROUPER:INS:0:620;chr2:GROUPER:INS:0:718;chr2:GROUPER:INS:0:764;chr2:GROUPER:INS:0:666;chr2:GROUPER:INS:0:693;chr2:GROUPER:INS:0:514;chr2:GROUPER:INS:0:789 A AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCT,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGC,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGGGGGG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCG,AGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCG 74 PASS NS=1;SVTYPE=INS;SVLEN=115;READSOURCES=(0:8);UPSTREAM=AAAAGCAAAGACTTGGAACCAACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATA;DOWNSTREAM=.;CONTIG=AAAAGCAAAGACTTGGAACCAACCTACATGTCCAACAAGGATAGACTGGATTAAGAAAATGTGGCACATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTGAAACCCCGTCTCT;CONTIG_NUM=842;CLUSTER_NUM=838;ensembl_gene_id=ENSG00000003393 GT 1/. ./. ./. ./. ./. ./. 2/. ./. 3/. ./. ./. ./. ./. ./. 4/. ./. ./. 5/. ./. ./. ./. ./. 6/. ./. ./. 5/. ./. ./. ./. ./. 2/. ./. 2/. ./. ./. 7/. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. 2/. ./. ./. 8/. ./. ./. ./. ./. ./. ./. ./. 9/. 10/. 11/. 12/. ./. ./. ./. 6/. -chr12 109280301 chr12:GROUPER:INS:0:2149 A AAGAAGCCTGAAGATGCAAGAGTGAGCGAGAAGGGAGGGAGTATGAGAGCAGCCAAGGCAAAAGTTCTAGAGAAGAAAGGTTGAATTTTTAAAGTTAGTTAGGAACAATAGAAGTTTGAAAAGGGGAAGCAG 1 PASS NS=1;SVTYPE=INS;SVLEN=131;READSOURCES=(0:2);UPSTREAM=GCAGTGA;DOWNSTREAM=.;CONTIG=GCAGTGAAGAAGCCTGAAGATGCAAGAGTGAGCGAGAAGGGAGGGAGTATGAGAGCAGCCAAGGCAAAAGTTCTAGAGAAGAAAGGTTGAATTTTTAAAGTTAGTTAGGAACAATAGAAGTTTGAAAAGGGGAAGCAG;CONTIG_NUM=2978;CLUSTER_NUM=2920;ensembl_gene_id=ENSG00000110887 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr12 109280509 chr12:GROUPER:INS:0:2448 t tGAACTTTTGAAAGCTATAGTATCTTCATGCTGAAATGCCAAGCTTCCATGAAGTGCTGAGAATAGCCTAGAAAACTCGTAGTGGGCAGGAGGAA 1 PASS NS=1;SVTYPE=INS;SVLEN=94;READSOURCES=(0:2);UPSTREAM=AGAGCTG;DOWNSTREAM=.;CONTIG=AGAGCTGAACTTTTGAAAGCTATAGTATCTTCATGCTGAAATGCCAAGCTTCCATGAAGTGCTGAGAATAGCCTAGAAAACTCGTAGTGGGCAGGAGGAAG;CONTIG_NUM=3870;CLUSTER_NUM=5188;ensembl_gene_id=ENSG00000110887 GT ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr12 109280301 chr12:GROUPER:INS:0:2149 A AAGAAGCCTGAAGATGCAAGAGTGAGCGAGAAGGGAGGGAGTATGAGAGCAGCCAAGGCAAAAGTTCTAGAGAAGAAAGGTTGAATTTTTAAAGTTAGTTAGGAACAATAGAAGTTTGAAAAGGGGAAGCAG 1 PASS NS=1;SVTYPE=INS;SVLEN=131;READSOURCES=(0:2);UPSTREAM=GCAGTGA;DOWNSTREAM=.;CONTIG=GCAGTGAAGAAGCCTGAAGATGCAAGAGTGAGCGAGAAGGGAGGGAGTATGAGAGCAGCCAAGGCAAAAGTTCTAGAGAAGAAAGGTTGAATTTTTAAAGTTAGTTAGGAACAATAGAAGTTTGAAAAGGGGAAGCAG;CONTIG_NUM=2978;CLUSTER_NUM=2920;ensembl_gene_id=ENSG00000110887 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr12 109280509 chr12:GROUPER:INS:0:2448 t tGAACTTTTGAAAGCTATAGTATCTTCATGCTGAAATGCCAAGCTTCCATGAAGTGCTGAGAATAGCCTAGAAAACTCGTAGTGGGCAGGAGGAA 1 PASS NS=1;SVTYPE=INS;SVLEN=94;READSOURCES=(0:2);UPSTREAM=AGAGCTG;DOWNSTREAM=.;CONTIG=AGAGCTGAACTTTTGAAAGCTATAGTATCTTCATGCTGAAATGCCAAGCTTCCATGAAGTGCTGAGAATAGCCTAGAAAACTCGTAGTGGGCAGGAGGAAG;CONTIG_NUM=3870;CLUSTER_NUM=5188;ensembl_gene_id=ENSG00000110887 GT ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr12 109280301 chr12:GROUPER:INS:0:2149 A AAGAAGCCTGAAGATGCAAGAGTGAGCGAGAAGGGAGGGAGTATGAGAGCAGCCAAGGCAAAAGTTCTAGAGAAGAAAGGTTGAATTTTTAAAGTTAGTTAGGAACAATAGAAGTTTGAAAAGGGGAAGCAG 1 PASS NS=1;SVTYPE=INS;SVLEN=131;READSOURCES=(0:2);UPSTREAM=GCAGTGA;DOWNSTREAM=.;CONTIG=GCAGTGAAGAAGCCTGAAGATGCAAGAGTGAGCGAGAAGGGAGGGAGTATGAGAGCAGCCAAGGCAAAAGTTCTAGAGAAGAAAGGTTGAATTTTTAAAGTTAGTTAGGAACAATAGAAGTTTGAAAAGGGGAAGCAG;CONTIG_NUM=2978;CLUSTER_NUM=2920;ensembl_gene_id=ENSG00000110887 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr12 109280509 chr12:GROUPER:INS:0:2448 t tGAACTTTTGAAAGCTATAGTATCTTCATGCTGAAATGCCAAGCTTCCATGAAGTGCTGAGAATAGCCTAGAAAACTCGTAGTGGGCAGGAGGAA 1 PASS NS=1;SVTYPE=INS;SVLEN=94;READSOURCES=(0:2);UPSTREAM=AGAGCTG;DOWNSTREAM=.;CONTIG=AGAGCTGAACTTTTGAAAGCTATAGTATCTTCATGCTGAAATGCCAAGCTTCCATGAAGTGCTGAGAATAGCCTAGAAAACTCGTAGTGGGCAGGAGGAAG;CONTIG_NUM=3870;CLUSTER_NUM=5188;ensembl_gene_id=ENSG00000110887 GT ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr12 109280301 chr12:GROUPER:INS:0:2149 A AAGAAGCCTGAAGATGCAAGAGTGAGCGAGAAGGGAGGGAGTATGAGAGCAGCCAAGGCAAAAGTTCTAGAGAAGAAAGGTTGAATTTTTAAAGTTAGTTAGGAACAATAGAAGTTTGAAAAGGGGAAGCAG 1 PASS NS=1;SVTYPE=INS;SVLEN=131;READSOURCES=(0:2);UPSTREAM=GCAGTGA;DOWNSTREAM=.;CONTIG=GCAGTGAAGAAGCCTGAAGATGCAAGAGTGAGCGAGAAGGGAGGGAGTATGAGAGCAGCCAAGGCAAAAGTTCTAGAGAAGAAAGGTTGAATTTTTAAAGTTAGTTAGGAACAATAGAAGTTTGAAAAGGGGAAGCAG;CONTIG_NUM=2978;CLUSTER_NUM=2920;ensembl_gene_id=ENSG00000110887 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr12 109280509 chr12:GROUPER:INS:0:2448 t tGAACTTTTGAAAGCTATAGTATCTTCATGCTGAAATGCCAAGCTTCCATGAAGTGCTGAGAATAGCCTAGAAAACTCGTAGTGGGCAGGAGGAA 1 PASS NS=1;SVTYPE=INS;SVLEN=94;READSOURCES=(0:2);UPSTREAM=AGAGCTG;DOWNSTREAM=.;CONTIG=AGAGCTGAACTTTTGAAAGCTATAGTATCTTCATGCTGAAATGCCAAGCTTCCATGAAGTGCTGAGAATAGCCTAGAAAACTCGTAGTGGGCAGGAGGAAG;CONTIG_NUM=3870;CLUSTER_NUM=5188;ensembl_gene_id=ENSG00000110887 GT ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr12 109280301 chr12:GROUPER:INS:0:2149 A AAGAAGCCTGAAGATGCAAGAGTGAGCGAGAAGGGAGGGAGTATGAGAGCAGCCAAGGCAAAAGTTCTAGAGAAGAAAGGTTGAATTTTTAAAGTTAGTTAGGAACAATAGAAGTTTGAAAAGGGGAAGCAG 1 PASS NS=1;SVTYPE=INS;SVLEN=131;READSOURCES=(0:2);UPSTREAM=GCAGTGA;DOWNSTREAM=.;CONTIG=GCAGTGAAGAAGCCTGAAGATGCAAGAGTGAGCGAGAAGGGAGGGAGTATGAGAGCAGCCAAGGCAAAAGTTCTAGAGAAGAAAGGTTGAATTTTTAAAGTTAGTTAGGAACAATAGAAGTTTGAAAAGGGGAAGCAG;CONTIG_NUM=2978;CLUSTER_NUM=2920;ensembl_gene_id=ENSG00000110887 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr12 109280509 chr12:GROUPER:INS:0:2448 t tGAACTTTTGAAAGCTATAGTATCTTCATGCTGAAATGCCAAGCTTCCATGAAGTGCTGAGAATAGCCTAGAAAACTCGTAGTGGGCAGGAGGAA 1 PASS NS=1;SVTYPE=INS;SVLEN=94;READSOURCES=(0:2);UPSTREAM=AGAGCTG;DOWNSTREAM=.;CONTIG=AGAGCTGAACTTTTGAAAGCTATAGTATCTTCATGCTGAAATGCCAAGCTTCCATGAAGTGCTGAGAATAGCCTAGAAAACTCGTAGTGGGCAGGAGGAAG;CONTIG_NUM=3870;CLUSTER_NUM=5188;ensembl_gene_id=ENSG00000110887 GT ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr12 109280301 chr12:GROUPER:INS:0:2149 A AAGAAGCCTGAAGATGCAAGAGTGAGCGAGAAGGGAGGGAGTATGAGAGCAGCCAAGGCAAAAGTTCTAGAGAAGAAAGGTTGAATTTTTAAAGTTAGTTAGGAACAATAGAAGTTTGAAAAGGGGAAGCAG 1 PASS NS=1;SVTYPE=INS;SVLEN=131;READSOURCES=(0:2);UPSTREAM=GCAGTGA;DOWNSTREAM=.;CONTIG=GCAGTGAAGAAGCCTGAAGATGCAAGAGTGAGCGAGAAGGGAGGGAGTATGAGAGCAGCCAAGGCAAAAGTTCTAGAGAAGAAAGGTTGAATTTTTAAAGTTAGTTAGGAACAATAGAAGTTTGAAAAGGGGAAGCAG;CONTIG_NUM=2978;CLUSTER_NUM=2920;ensembl_gene_id=ENSG00000110887 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr12 109280509 chr12:GROUPER:INS:0:2448 t tGAACTTTTGAAAGCTATAGTATCTTCATGCTGAAATGCCAAGCTTCCATGAAGTGCTGAGAATAGCCTAGAAAACTCGTAGTGGGCAGGAGGAA 1 PASS NS=1;SVTYPE=INS;SVLEN=94;READSOURCES=(0:2);UPSTREAM=AGAGCTG;DOWNSTREAM=.;CONTIG=AGAGCTGAACTTTTGAAAGCTATAGTATCTTCATGCTGAAATGCCAAGCTTCCATGAAGTGCTGAGAATAGCCTAGAAAACTCGTAGTGGGCAGGAGGAAG;CONTIG_NUM=3870;CLUSTER_NUM=5188;ensembl_gene_id=ENSG00000110887 GT ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr12 109280301 chr12:GROUPER:INS:0:2149 A AAGAAGCCTGAAGATGCAAGAGTGAGCGAGAAGGGAGGGAGTATGAGAGCAGCCAAGGCAAAAGTTCTAGAGAAGAAAGGTTGAATTTTTAAAGTTAGTTAGGAACAATAGAAGTTTGAAAAGGGGAAGCAG 1 PASS NS=1;SVTYPE=INS;SVLEN=131;READSOURCES=(0:2);UPSTREAM=GCAGTGA;DOWNSTREAM=.;CONTIG=GCAGTGAAGAAGCCTGAAGATGCAAGAGTGAGCGAGAAGGGAGGGAGTATGAGAGCAGCCAAGGCAAAAGTTCTAGAGAAGAAAGGTTGAATTTTTAAAGTTAGTTAGGAACAATAGAAGTTTGAAAAGGGGAAGCAG;CONTIG_NUM=2978;CLUSTER_NUM=2920;ensembl_gene_id=ENSG00000110887 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr12 109280509 chr12:GROUPER:INS:0:2448 t tGAACTTTTGAAAGCTATAGTATCTTCATGCTGAAATGCCAAGCTTCCATGAAGTGCTGAGAATAGCCTAGAAAACTCGTAGTGGGCAGGAGGAA 1 PASS NS=1;SVTYPE=INS;SVLEN=94;READSOURCES=(0:2);UPSTREAM=AGAGCTG;DOWNSTREAM=.;CONTIG=AGAGCTGAACTTTTGAAAGCTATAGTATCTTCATGCTGAAATGCCAAGCTTCCATGAAGTGCTGAGAATAGCCTAGAAAACTCGTAGTGGGCAGGAGGAAG;CONTIG_NUM=3870;CLUSTER_NUM=5188;ensembl_gene_id=ENSG00000110887 GT ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110039896 chr6:GROUPER:DEL:0:3060 TGTTGAATGGATGAGTGTTTGTGGGAATGTGTATGTCTGTATGTGTCACGTGAGTTCATGTGCTTAAATGCCATAAATGCCAGTATGTTAAATTCCACTTTCAGTCCTGCTTATATTTTAAATTTAAGAAAAAAATACTGTAAATAAAATGTGTTTAAAATATAGTAGACTCTAATTTAAATAATAGTTACTTAATAGTTTAAGCTTAAATGTTGATACCTTATTACA T 31 PASS NS=1;SVTYPE=DEL;SVLEN=-227;READSOURCES=(0:5);UPSTREAM=TTACAT;DOWNSTREAM=TTTTTTTTTTTTTTTTGAGACAGAGCCTTGCTGTGTC;CONTIG=TTACATTTTTTTTTTTTTTTTTGAGACAGAGCCTTGCTGTGTC;CONTIG_NUM=4513;CLUSTER_NUM=5505;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110070170 chr6:GROUPER:INS:0:2977 c cAGAGGCCGAGGCAGGAGGATCACTTGAGTATAGTATATATAAAAATATAAAATGAAGGAAGGGGCCGGGCACAAGGGCTCACACCTGTA 36 PASS NS=1;SVTYPE=INS;SVLEN=89;READSOURCES=(0:2);UPSTREAM=GAATTACGGGAGCTACAATTCAAAATGAGCTTTGGGTGGGGACACAGCCAAACCATGTCA;DOWNSTREAM=.;CONTIG=GAATTACGGGAGCTACAATTCAAAATGAGCTTTGGGTGGGGACACAGCCAAACCATGTCAGAGGCCGAGGCAGGAGGATCACTTGAGTATAGTATATATAAAAATATAAAATGAAGGAAGGGGCCGGGCACAAGGGCTCACACCTGTAA;CONTIG_NUM=4516;CLUSTER_NUM=5647;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. -chr6 110070171 chr6:GROUPER:INS:0:2648 A AGAGGCCGAGGCAGGAGGATCACTTGAGTATAGTATATATAAAAATATAAAATGAAGGAAGGGGCCGGGCACAAGGGCTCAC 30 PASS NS=1;SVTYPE=INS;SVLEN=81;READSOURCES=(0:2);UPSTREAM=CTACAATTCAAAATGAGCTTTGGGTGGGGACACAGCCAAACCATGTCA;DOWNSTREAM=.;CONTIG=CTACAATTCAAAATGAGCTTTGGGTGGGGACACAGCCAAACCATGTCAGAGGCCGAGGCAGGAGGATCACTTGAGTATAGTATATATAAAAATATAAAATGAAGGAAGGGGCCGGGCACAAGGGCTCAC;CONTIG_NUM=4035;CLUSTER_NUM=4950;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110077118 chr6:GROUPER:INS:0:3021 T TCCCAAGCAGCCTAACTGGGAGGCACCCCCATCAGGGGCAGACTGACACCTCACATGGCCGGGTACTCCAACAGACCTGCAGCTGAGGGTCCTGTCTGTGAGAAAGAA 27 PASS NS=1;SVTYPE=INS;SVLEN=107;READSOURCES=(0:2);UPSTREAM=CTCTTTATCCAACTTGCCAGTCTGTGTCTTTTAATT;DOWNSTREAM=.;CONTIG=CTCTTTATCCAACTTGCCAGTCTGTGTCTTTTAATTCCCAAGCAGCCTAACTGGGAGGCACCCCCATCAGGGGCAGACTGACACCTCACATGGCCGGGTACTCCAACAGACCTGCAGCTGAGGGTCCTGTCTGTGAGAAAGAA;CONTIG_NUM=4599;CLUSTER_NUM=5477;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110078130 chr6:GROUPER:INS:0:3070 t tTGGAGGAGGAGAGGCGCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTT 1 PASS NS=1;SVTYPE=INS;SVLEN=83;READSOURCES=(0:3);UPSTREAM=TTCCTTT;DOWNSTREAM=.;CONTIG=TTCCTTTGGAGGAGGAGAGGCGCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTTT;CONTIG_NUM=4632;CLUSTER_NUM=5633;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110078194 chr6:GROUPER:INS:0:2576 c cTTTGGAGGAGGAGAGGCGCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTTTTGGTCTTTGATGATGGTGATGTACAGATGGGTT 17 PASS NS=1;SVTYPE=INS;SVLEN=119;READSOURCES=(0:3);UPSTREAM=TTGTTCCGTTGCTGGTGAGGAGCTGCGTTCCT;DOWNSTREAM=.;CONTIG=TTGTTCCGTTGCTGGTGAGGAGCTGCGTTCCTTTGGAGGAGGAGAGGCGCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTTTTGGTCTTTGATGATGGTGATGTACAGATGGGTTT;CONTIG_NUM=3746;CLUSTER_NUM=3651;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110078195 chr6:GROUPER:INS:0:3110 T TTTGGAGGAGGAGAGGCGCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTTTTGGTCTTTGATGATGGTGATGTACAGATGGGTTTTTGGTGTGGATGTCCTTTCTGTTTGTTAGTTTTCCTTGTAACAGACAGGA 12 PASS NS=1;SVTYPE=INS;SVLEN=169;READSOURCES=(0:5);UPSTREAM=TTGCTGGTGAGGAGCTGCGTTCCT;DOWNSTREAM=.;CONTIG=TTGCTGGTGAGGAGCTGCGTTCCTTTGGAGGAGGAGAGGCGCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTTTTGGTCTTTGATGATGGTGATGTACAGATGGGTTTTTGGTGTGGATGTCCTTTCTGTTTGTTAGTTTTCCTTGTAACAGACAGGA;CONTIG_NUM=4913;CLUSTER_NUM=6061;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. -chr6 110102976 chr6:GROUPER:INS:0:3050 C CAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCTGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAAAGTGCT 70 PASS NS=1;SVTYPE=INS;SVLEN=287;READSOURCES=(0:27);UPSTREAM=GCTTTTTATTTTTTTC;DOWNSTREAM=AGATTTAATCAGTTGACCATCTTGATCCTAATTCAAGTACTTGATGAAAAATGTTGAGTACAGTAGGGTAAATGG;CONTIG=GCTTTTTATTTTTTTCAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCTGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAAAGTGCTAGATTTAATCAGTTGACCATCTTGATCCTAATTCAAGTACTTGATGAAAAATGTTGAGTACAGTAGGGTAAATGG;CONTIG_NUM=4041;CLUSTER_NUM=3943;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110102981 chr6:GROUPER:INS:0:3030;chr6:GROUPER:INS:0:2898;chr6:GROUPER:INS:0:2943;chr6:GROUPER:INS:0:3115;chr6:GROUPER:INS:0:2878;chr6:GROUPER:INS:0:2936;chr6:GROUPER:INS:0:2572;chr6:GROUPER:INS:0:2817;chr6:GROUPER:INS:0:2952 t tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 67 PASS NS=1;SVTYPE=INS;SVLEN=53;READSOURCES=(0:2);UPSTREAM=ATAGTTTCTTCAGATTT;DOWNSTREAM=.;CONTIG=ATAGTTTCTTCAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT;CONTIG_NUM=4615;CLUSTER_NUM=5491;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. 2/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 3/. ./. ./. ./. ./. ./. ./. 2/. 2/. ./. ./. 4/. 5/. ./. ./. ./. 2/. 1/. ./. -chr6 110102982 chr6:GROUPER:INS:0:3076 T TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATCTGCTGTTCTGTCTTGCCCCC 44 PASS NS=1;SVTYPE=INS;SVLEN=76;READSOURCES=(0:2);UPSTREAM=AAATGTGTACCTTTAATGAATACTTCTAGCTTTATAGTTTCTTCAGATTT;DOWNSTREAM=.;CONTIG=AAATGTGTACCTTTAATGAATACTTCTAGCTTTATAGTTTCTTCAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATCTGCTGTTCTGTCTTGCCCCC;CONTIG_NUM=4646;CLUSTER_NUM=5643;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110121295 chr6:GROUPER:INS:0:2978 g gAGGGGAAAGTGACTTGTCTGAAGTTGTATAGTGACTGAGACACAAACCCAAGACACAAACTGCTT 29 PASS NS=1;SVTYPE=INS;SVLEN=65;READSOURCES=(0:2);UPSTREAM=TCCATTTTACAGATGGGGAAACTGAGGCACAGAGA;DOWNSTREAM=.;CONTIG=TCCATTTTACAGATGGGGAAACTGAGGCACAGAGAGGGGAAAGTGACTTGTCTGAAGTTGTATAGTGACTGAGACACAAACCCAAGACACAAACTGCTTA;CONTIG_NUM=4485;CLUSTER_NUM=5608;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110039896 chr6:GROUPER:DEL:0:3060 TGTTGAATGGATGAGTGTTTGTGGGAATGTGTATGTCTGTATGTGTCACGTGAGTTCATGTGCTTAAATGCCATAAATGCCAGTATGTTAAATTCCACTTTCAGTCCTGCTTATATTTTAAATTTAAGAAAAAAATACTGTAAATAAAATGTGTTTAAAATATAGTAGACTCTAATTTAAATAATAGTTACTTAATAGTTTAAGCTTAAATGTTGATACCTTATTACA T 31 PASS NS=1;SVTYPE=DEL;SVLEN=-227;READSOURCES=(0:5);UPSTREAM=TTACAT;DOWNSTREAM=TTTTTTTTTTTTTTTTGAGACAGAGCCTTGCTGTGTC;CONTIG=TTACATTTTTTTTTTTTTTTTTGAGACAGAGCCTTGCTGTGTC;CONTIG_NUM=4513;CLUSTER_NUM=5505;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110070170 chr6:GROUPER:INS:0:2977 c cAGAGGCCGAGGCAGGAGGATCACTTGAGTATAGTATATATAAAAATATAAAATGAAGGAAGGGGCCGGGCACAAGGGCTCACACCTGTA 36 PASS NS=1;SVTYPE=INS;SVLEN=89;READSOURCES=(0:2);UPSTREAM=GAATTACGGGAGCTACAATTCAAAATGAGCTTTGGGTGGGGACACAGCCAAACCATGTCA;DOWNSTREAM=.;CONTIG=GAATTACGGGAGCTACAATTCAAAATGAGCTTTGGGTGGGGACACAGCCAAACCATGTCAGAGGCCGAGGCAGGAGGATCACTTGAGTATAGTATATATAAAAATATAAAATGAAGGAAGGGGCCGGGCACAAGGGCTCACACCTGTAA;CONTIG_NUM=4516;CLUSTER_NUM=5647;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. -chr6 110070171 chr6:GROUPER:INS:0:2648 A AGAGGCCGAGGCAGGAGGATCACTTGAGTATAGTATATATAAAAATATAAAATGAAGGAAGGGGCCGGGCACAAGGGCTCAC 30 PASS NS=1;SVTYPE=INS;SVLEN=81;READSOURCES=(0:2);UPSTREAM=CTACAATTCAAAATGAGCTTTGGGTGGGGACACAGCCAAACCATGTCA;DOWNSTREAM=.;CONTIG=CTACAATTCAAAATGAGCTTTGGGTGGGGACACAGCCAAACCATGTCAGAGGCCGAGGCAGGAGGATCACTTGAGTATAGTATATATAAAAATATAAAATGAAGGAAGGGGCCGGGCACAAGGGCTCAC;CONTIG_NUM=4035;CLUSTER_NUM=4950;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110077118 chr6:GROUPER:INS:0:3021 T TCCCAAGCAGCCTAACTGGGAGGCACCCCCATCAGGGGCAGACTGACACCTCACATGGCCGGGTACTCCAACAGACCTGCAGCTGAGGGTCCTGTCTGTGAGAAAGAA 27 PASS NS=1;SVTYPE=INS;SVLEN=107;READSOURCES=(0:2);UPSTREAM=CTCTTTATCCAACTTGCCAGTCTGTGTCTTTTAATT;DOWNSTREAM=.;CONTIG=CTCTTTATCCAACTTGCCAGTCTGTGTCTTTTAATTCCCAAGCAGCCTAACTGGGAGGCACCCCCATCAGGGGCAGACTGACACCTCACATGGCCGGGTACTCCAACAGACCTGCAGCTGAGGGTCCTGTCTGTGAGAAAGAA;CONTIG_NUM=4599;CLUSTER_NUM=5477;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110078130 chr6:GROUPER:INS:0:3070 t tTGGAGGAGGAGAGGCGCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTT 1 PASS NS=1;SVTYPE=INS;SVLEN=83;READSOURCES=(0:3);UPSTREAM=TTCCTTT;DOWNSTREAM=.;CONTIG=TTCCTTTGGAGGAGGAGAGGCGCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTTT;CONTIG_NUM=4632;CLUSTER_NUM=5633;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110078194 chr6:GROUPER:INS:0:2576 c cTTTGGAGGAGGAGAGGCGCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTTTTGGTCTTTGATGATGGTGATGTACAGATGGGTT 17 PASS NS=1;SVTYPE=INS;SVLEN=119;READSOURCES=(0:3);UPSTREAM=TTGTTCCGTTGCTGGTGAGGAGCTGCGTTCCT;DOWNSTREAM=.;CONTIG=TTGTTCCGTTGCTGGTGAGGAGCTGCGTTCCTTTGGAGGAGGAGAGGCGCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTTTTGGTCTTTGATGATGGTGATGTACAGATGGGTTT;CONTIG_NUM=3746;CLUSTER_NUM=3651;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110078195 chr6:GROUPER:INS:0:3110 T TTTGGAGGAGGAGAGGCGCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTTTTGGTCTTTGATGATGGTGATGTACAGATGGGTTTTTGGTGTGGATGTCCTTTCTGTTTGTTAGTTTTCCTTGTAACAGACAGGA 12 PASS NS=1;SVTYPE=INS;SVLEN=169;READSOURCES=(0:5);UPSTREAM=TTGCTGGTGAGGAGCTGCGTTCCT;DOWNSTREAM=.;CONTIG=TTGCTGGTGAGGAGCTGCGTTCCTTTGGAGGAGGAGAGGCGCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTTTTGGTCTTTGATGATGGTGATGTACAGATGGGTTTTTGGTGTGGATGTCCTTTCTGTTTGTTAGTTTTCCTTGTAACAGACAGGA;CONTIG_NUM=4913;CLUSTER_NUM=6061;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. -chr6 110102976 chr6:GROUPER:INS:0:3050 C CAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCTGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAAAGTGCT 70 PASS NS=1;SVTYPE=INS;SVLEN=287;READSOURCES=(0:27);UPSTREAM=GCTTTTTATTTTTTTC;DOWNSTREAM=AGATTTAATCAGTTGACCATCTTGATCCTAATTCAAGTACTTGATGAAAAATGTTGAGTACAGTAGGGTAAATGG;CONTIG=GCTTTTTATTTTTTTCAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCTGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAAAGTGCTAGATTTAATCAGTTGACCATCTTGATCCTAATTCAAGTACTTGATGAAAAATGTTGAGTACAGTAGGGTAAATGG;CONTIG_NUM=4041;CLUSTER_NUM=3943;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110102981 chr6:GROUPER:INS:0:3030;chr6:GROUPER:INS:0:2898;chr6:GROUPER:INS:0:2943;chr6:GROUPER:INS:0:3115;chr6:GROUPER:INS:0:2878;chr6:GROUPER:INS:0:2936;chr6:GROUPER:INS:0:2572;chr6:GROUPER:INS:0:2817;chr6:GROUPER:INS:0:2952 t tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 67 PASS NS=1;SVTYPE=INS;SVLEN=53;READSOURCES=(0:2);UPSTREAM=ATAGTTTCTTCAGATTT;DOWNSTREAM=.;CONTIG=ATAGTTTCTTCAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT;CONTIG_NUM=4615;CLUSTER_NUM=5491;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. 2/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 3/. ./. ./. ./. ./. ./. ./. 2/. 2/. ./. ./. 4/. 5/. ./. ./. ./. 2/. 1/. ./. -chr6 110102982 chr6:GROUPER:INS:0:3076 T TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATCTGCTGTTCTGTCTTGCCCCC 44 PASS NS=1;SVTYPE=INS;SVLEN=76;READSOURCES=(0:2);UPSTREAM=AAATGTGTACCTTTAATGAATACTTCTAGCTTTATAGTTTCTTCAGATTT;DOWNSTREAM=.;CONTIG=AAATGTGTACCTTTAATGAATACTTCTAGCTTTATAGTTTCTTCAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATCTGCTGTTCTGTCTTGCCCCC;CONTIG_NUM=4646;CLUSTER_NUM=5643;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110121295 chr6:GROUPER:INS:0:2978 g gAGGGGAAAGTGACTTGTCTGAAGTTGTATAGTGACTGAGACACAAACCCAAGACACAAACTGCTT 29 PASS NS=1;SVTYPE=INS;SVLEN=65;READSOURCES=(0:2);UPSTREAM=TCCATTTTACAGATGGGGAAACTGAGGCACAGAGA;DOWNSTREAM=.;CONTIG=TCCATTTTACAGATGGGGAAACTGAGGCACAGAGAGGGGAAAGTGACTTGTCTGAAGTTGTATAGTGACTGAGACACAAACCCAAGACACAAACTGCTTA;CONTIG_NUM=4485;CLUSTER_NUM=5608;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110039896 chr6:GROUPER:DEL:0:3060 TGTTGAATGGATGAGTGTTTGTGGGAATGTGTATGTCTGTATGTGTCACGTGAGTTCATGTGCTTAAATGCCATAAATGCCAGTATGTTAAATTCCACTTTCAGTCCTGCTTATATTTTAAATTTAAGAAAAAAATACTGTAAATAAAATGTGTTTAAAATATAGTAGACTCTAATTTAAATAATAGTTACTTAATAGTTTAAGCTTAAATGTTGATACCTTATTACA T 31 PASS NS=1;SVTYPE=DEL;SVLEN=-227;READSOURCES=(0:5);UPSTREAM=TTACAT;DOWNSTREAM=TTTTTTTTTTTTTTTTGAGACAGAGCCTTGCTGTGTC;CONTIG=TTACATTTTTTTTTTTTTTTTTGAGACAGAGCCTTGCTGTGTC;CONTIG_NUM=4513;CLUSTER_NUM=5505;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110070170 chr6:GROUPER:INS:0:2977 c cAGAGGCCGAGGCAGGAGGATCACTTGAGTATAGTATATATAAAAATATAAAATGAAGGAAGGGGCCGGGCACAAGGGCTCACACCTGTA 36 PASS NS=1;SVTYPE=INS;SVLEN=89;READSOURCES=(0:2);UPSTREAM=GAATTACGGGAGCTACAATTCAAAATGAGCTTTGGGTGGGGACACAGCCAAACCATGTCA;DOWNSTREAM=.;CONTIG=GAATTACGGGAGCTACAATTCAAAATGAGCTTTGGGTGGGGACACAGCCAAACCATGTCAGAGGCCGAGGCAGGAGGATCACTTGAGTATAGTATATATAAAAATATAAAATGAAGGAAGGGGCCGGGCACAAGGGCTCACACCTGTAA;CONTIG_NUM=4516;CLUSTER_NUM=5647;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. -chr6 110070171 chr6:GROUPER:INS:0:2648 A AGAGGCCGAGGCAGGAGGATCACTTGAGTATAGTATATATAAAAATATAAAATGAAGGAAGGGGCCGGGCACAAGGGCTCAC 30 PASS NS=1;SVTYPE=INS;SVLEN=81;READSOURCES=(0:2);UPSTREAM=CTACAATTCAAAATGAGCTTTGGGTGGGGACACAGCCAAACCATGTCA;DOWNSTREAM=.;CONTIG=CTACAATTCAAAATGAGCTTTGGGTGGGGACACAGCCAAACCATGTCAGAGGCCGAGGCAGGAGGATCACTTGAGTATAGTATATATAAAAATATAAAATGAAGGAAGGGGCCGGGCACAAGGGCTCAC;CONTIG_NUM=4035;CLUSTER_NUM=4950;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110077118 chr6:GROUPER:INS:0:3021 T TCCCAAGCAGCCTAACTGGGAGGCACCCCCATCAGGGGCAGACTGACACCTCACATGGCCGGGTACTCCAACAGACCTGCAGCTGAGGGTCCTGTCTGTGAGAAAGAA 27 PASS NS=1;SVTYPE=INS;SVLEN=107;READSOURCES=(0:2);UPSTREAM=CTCTTTATCCAACTTGCCAGTCTGTGTCTTTTAATT;DOWNSTREAM=.;CONTIG=CTCTTTATCCAACTTGCCAGTCTGTGTCTTTTAATTCCCAAGCAGCCTAACTGGGAGGCACCCCCATCAGGGGCAGACTGACACCTCACATGGCCGGGTACTCCAACAGACCTGCAGCTGAGGGTCCTGTCTGTGAGAAAGAA;CONTIG_NUM=4599;CLUSTER_NUM=5477;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110078130 chr6:GROUPER:INS:0:3070 t tTGGAGGAGGAGAGGCGCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTT 1 PASS NS=1;SVTYPE=INS;SVLEN=83;READSOURCES=(0:3);UPSTREAM=TTCCTTT;DOWNSTREAM=.;CONTIG=TTCCTTTGGAGGAGGAGAGGCGCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTTT;CONTIG_NUM=4632;CLUSTER_NUM=5633;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110078194 chr6:GROUPER:INS:0:2576 c cTTTGGAGGAGGAGAGGCGCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTTTTGGTCTTTGATGATGGTGATGTACAGATGGGTT 17 PASS NS=1;SVTYPE=INS;SVLEN=119;READSOURCES=(0:3);UPSTREAM=TTGTTCCGTTGCTGGTGAGGAGCTGCGTTCCT;DOWNSTREAM=.;CONTIG=TTGTTCCGTTGCTGGTGAGGAGCTGCGTTCCTTTGGAGGAGGAGAGGCGCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTTTTGGTCTTTGATGATGGTGATGTACAGATGGGTTT;CONTIG_NUM=3746;CLUSTER_NUM=3651;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110078195 chr6:GROUPER:INS:0:3110 T TTTGGAGGAGGAGAGGCGCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTTTTGGTCTTTGATGATGGTGATGTACAGATGGGTTTTTGGTGTGGATGTCCTTTCTGTTTGTTAGTTTTCCTTGTAACAGACAGGA 12 PASS NS=1;SVTYPE=INS;SVLEN=169;READSOURCES=(0:5);UPSTREAM=TTGCTGGTGAGGAGCTGCGTTCCT;DOWNSTREAM=.;CONTIG=TTGCTGGTGAGGAGCTGCGTTCCTTTGGAGGAGGAGAGGCGCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTTTTGGTCTTTGATGATGGTGATGTACAGATGGGTTTTTGGTGTGGATGTCCTTTCTGTTTGTTAGTTTTCCTTGTAACAGACAGGA;CONTIG_NUM=4913;CLUSTER_NUM=6061;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. -chr6 110102976 chr6:GROUPER:INS:0:3050 C CAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCTGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAAAGTGCT 70 PASS NS=1;SVTYPE=INS;SVLEN=287;READSOURCES=(0:27);UPSTREAM=GCTTTTTATTTTTTTC;DOWNSTREAM=AGATTTAATCAGTTGACCATCTTGATCCTAATTCAAGTACTTGATGAAAAATGTTGAGTACAGTAGGGTAAATGG;CONTIG=GCTTTTTATTTTTTTCAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCTGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAAAGTGCTAGATTTAATCAGTTGACCATCTTGATCCTAATTCAAGTACTTGATGAAAAATGTTGAGTACAGTAGGGTAAATGG;CONTIG_NUM=4041;CLUSTER_NUM=3943;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110102981 chr6:GROUPER:INS:0:3030;chr6:GROUPER:INS:0:2898;chr6:GROUPER:INS:0:2943;chr6:GROUPER:INS:0:3115;chr6:GROUPER:INS:0:2878;chr6:GROUPER:INS:0:2936;chr6:GROUPER:INS:0:2572;chr6:GROUPER:INS:0:2817;chr6:GROUPER:INS:0:2952 t tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 67 PASS NS=1;SVTYPE=INS;SVLEN=53;READSOURCES=(0:2);UPSTREAM=ATAGTTTCTTCAGATTT;DOWNSTREAM=.;CONTIG=ATAGTTTCTTCAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT;CONTIG_NUM=4615;CLUSTER_NUM=5491;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. 2/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 3/. ./. ./. ./. ./. ./. ./. 2/. 2/. ./. ./. 4/. 5/. ./. ./. ./. 2/. 1/. ./. -chr6 110102982 chr6:GROUPER:INS:0:3076 T TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATCTGCTGTTCTGTCTTGCCCCC 44 PASS NS=1;SVTYPE=INS;SVLEN=76;READSOURCES=(0:2);UPSTREAM=AAATGTGTACCTTTAATGAATACTTCTAGCTTTATAGTTTCTTCAGATTT;DOWNSTREAM=.;CONTIG=AAATGTGTACCTTTAATGAATACTTCTAGCTTTATAGTTTCTTCAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATCTGCTGTTCTGTCTTGCCCCC;CONTIG_NUM=4646;CLUSTER_NUM=5643;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110121295 chr6:GROUPER:INS:0:2978 g gAGGGGAAAGTGACTTGTCTGAAGTTGTATAGTGACTGAGACACAAACCCAAGACACAAACTGCTT 29 PASS NS=1;SVTYPE=INS;SVLEN=65;READSOURCES=(0:2);UPSTREAM=TCCATTTTACAGATGGGGAAACTGAGGCACAGAGA;DOWNSTREAM=.;CONTIG=TCCATTTTACAGATGGGGAAACTGAGGCACAGAGAGGGGAAAGTGACTTGTCTGAAGTTGTATAGTGACTGAGACACAAACCCAAGACACAAACTGCTTA;CONTIG_NUM=4485;CLUSTER_NUM=5608;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110039896 chr6:GROUPER:DEL:0:3060 TGTTGAATGGATGAGTGTTTGTGGGAATGTGTATGTCTGTATGTGTCACGTGAGTTCATGTGCTTAAATGCCATAAATGCCAGTATGTTAAATTCCACTTTCAGTCCTGCTTATATTTTAAATTTAAGAAAAAAATACTGTAAATAAAATGTGTTTAAAATATAGTAGACTCTAATTTAAATAATAGTTACTTAATAGTTTAAGCTTAAATGTTGATACCTTATTACA T 31 PASS NS=1;SVTYPE=DEL;SVLEN=-227;READSOURCES=(0:5);UPSTREAM=TTACAT;DOWNSTREAM=TTTTTTTTTTTTTTTTGAGACAGAGCCTTGCTGTGTC;CONTIG=TTACATTTTTTTTTTTTTTTTTGAGACAGAGCCTTGCTGTGTC;CONTIG_NUM=4513;CLUSTER_NUM=5505;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110039896 chr6:GROUPER:DEL:0:3060 TGTTGAATGGATGAGTGTTTGTGGGAATGTGTATGTCTGTATGTGTCACGTGAGTTCATGTGCTTAAATGCCATAAATGCCAGTATGTTAAATTCCACTTTCAGTCCTGCTTATATTTTAAATTTAAGAAAAAAATACTGTAAATAAAATGTGTTTAAAATATAGTAGACTCTAATTTAAATAATAGTTACTTAATAGTTTAAGCTTAAATGTTGATACCTTATTACA T 31 PASS NS=1;SVTYPE=DEL;SVLEN=-227;READSOURCES=(0:5);UPSTREAM=TTACAT;DOWNSTREAM=TTTTTTTTTTTTTTTTGAGACAGAGCCTTGCTGTGTC;CONTIG=TTACATTTTTTTTTTTTTTTTTGAGACAGAGCCTTGCTGTGTC;CONTIG_NUM=4513;CLUSTER_NUM=5505;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110102976 chr6:GROUPER:INS:0:3050 C CAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCTGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAAAGTGCT 70 PASS NS=1;SVTYPE=INS;SVLEN=287;READSOURCES=(0:27);UPSTREAM=GCTTTTTATTTTTTTC;DOWNSTREAM=AGATTTAATCAGTTGACCATCTTGATCCTAATTCAAGTACTTGATGAAAAATGTTGAGTACAGTAGGGTAAATGG;CONTIG=GCTTTTTATTTTTTTCAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCTGCCACCGCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAAAGTGCTAGATTTAATCAGTTGACCATCTTGATCCTAATTCAAGTACTTGATGAAAAATGTTGAGTACAGTAGGGTAAATGG;CONTIG_NUM=4041;CLUSTER_NUM=3943;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr6 110102981 chr6:GROUPER:INS:0:3030;chr6:GROUPER:INS:0:2898;chr6:GROUPER:INS:0:2943;chr6:GROUPER:INS:0:3115;chr6:GROUPER:INS:0:2878;chr6:GROUPER:INS:0:2936;chr6:GROUPER:INS:0:2572;chr6:GROUPER:INS:0:2817;chr6:GROUPER:INS:0:2952 t tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT,tTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 67 PASS NS=1;SVTYPE=INS;SVLEN=53;READSOURCES=(0:2);UPSTREAM=ATAGTTTCTTCAGATTT;DOWNSTREAM=.;CONTIG=ATAGTTTCTTCAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT;CONTIG_NUM=4615;CLUSTER_NUM=5491;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. 2/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 3/. ./. ./. ./. ./. ./. ./. 2/. 2/. ./. ./. 4/. 5/. ./. ./. ./. 2/. 1/. ./. -chr6 110102982 chr6:GROUPER:INS:0:3076 T TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATCTGCTGTTCTGTCTTGCCCCC 44 PASS NS=1;SVTYPE=INS;SVLEN=76;READSOURCES=(0:2);UPSTREAM=AAATGTGTACCTTTAATGAATACTTCTAGCTTTATAGTTTCTTCAGATTT;DOWNSTREAM=.;CONTIG=AAATGTGTACCTTTAATGAATACTTCTAGCTTTATAGTTTCTTCAGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATCTGCTGTTCTGTCTTGCCCCC;CONTIG_NUM=4646;CLUSTER_NUM=5643;ensembl_gene_id=ENSG00000112367 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr22 29885585 chr22:GROUPER:DEL:0:5578;chr22:GROUPER:DEL:0:5588;chr22:GROUPER:DEL:0:5284;chr22:GROUPER:DEL:0:5730;chr22:GROUPER:DEL:0:4909;chr22:GROUPER:DEL:0:5202;chr22:GROUPER:DEL:0:5758;chr22:GROUPER:DEL:0:5498;chr22:GROUPER:DEL:0:5216;chr22:GROUPER:DEL:0:5345;chr22:GROUPER:DEL:0:5276;chr22:GROUPER:DEL:0:5859;chr22:GROUPER:DEL:0:4589;chr22:GROUPER:DEL:0:5392;chr22:GROUPER:DEL:0:5461;chr22:GROUPER:DEL:0:4561;chr22:GROUPER:DEL:0:5825;chr22:GROUPER:DEL:0:5395;chr22:GROUPER:DEL:0:4917;chr22:GROUPER:DEL:0:4957;chr22:GROUPER:DEL:0:4764;chr22:GROUPER:DEL:0:4870;chr22:GROUPER:DEL:0:5626;chr22:GROUPER:DEL:0:5391;chr22:GROUPER:DEL:0:5330;chr22:GROUPER:DEL:0:5507;chr22:GROUPER:DEL:0:5024;chr22:GROUPER:DEL:0:5635;chr22:GROUPER:DEL:0:5151 CAAGTCCCCAGAGAAGGAAGAGGCCAAGTCCCCTGAGAAGGCCAAGTCCCCAGTGAAGGCAGAAGCAAAGTCCCCTGAGAAGGCCAAGTCCCCAGTGAAGGCAGAAGCA C 139 PASS NS=1;SVTYPE=DEL;SVLEN=-108;READSOURCES=(0:4);UPSTREAM=CAGCTGAGGTCAAGTCCCCGGAAAAGGCCAAGTCTCCAACGAAGGAGGAAGCAAAGTCCCCTGAGAAGGCC;DOWNSTREAM=AAGTCCCCTGAGAAGGCCAAGTCCCCAGAGAAGGAAGAGGCCAAGTCC;CONTIG=CAGCTGAGGTCAAGTCCCCGGAAAAGGCCAAGTCTCCAACGAAGGAGGAAGCAAAGTCCCCTGAGAAGGCCAAGTCCCCTGAGAAGGCCAAGTCCCCAGAGAAGGAAGAGGCCAAGTCC;CONTIG_NUM=10649;CLUSTER_NUM=10577;ensembl_gene_id=ENSG00000100285 GT ./. ./. ./. ./. 1/. 1/. ./. 1/. 1/. ./. ./. ./. ./. ./. 1/. 1/. ./. 1/. 1/. ./. ./. 1/. 1/. ./. ./. 1/. 1/. ./. 1/. 1/. 1/. 1/. 1/. 1/. ./. 1/. ./. ./. ./. ./. ./. ./. 1/. ./. 1/. 1/. ./. 1/. 1/. ./. 1/. ./. ./. ./. ./. 1/. ./. ./. 1/. ./. ./. ./. 1/. ./. ./. 1/. ./. -chr22 29885585 chr22:GROUPER:DEL:0:5578;chr22:GROUPER:DEL:0:5588;chr22:GROUPER:DEL:0:5284;chr22:GROUPER:DEL:0:5730;chr22:GROUPER:DEL:0:4909;chr22:GROUPER:DEL:0:5202;chr22:GROUPER:DEL:0:5758;chr22:GROUPER:DEL:0:5498;chr22:GROUPER:DEL:0:5216;chr22:GROUPER:DEL:0:5345;chr22:GROUPER:DEL:0:5276;chr22:GROUPER:DEL:0:5859;chr22:GROUPER:DEL:0:4589;chr22:GROUPER:DEL:0:5392;chr22:GROUPER:DEL:0:5461;chr22:GROUPER:DEL:0:4561;chr22:GROUPER:DEL:0:5825;chr22:GROUPER:DEL:0:5395;chr22:GROUPER:DEL:0:4917;chr22:GROUPER:DEL:0:4957;chr22:GROUPER:DEL:0:4764;chr22:GROUPER:DEL:0:4870;chr22:GROUPER:DEL:0:5626;chr22:GROUPER:DEL:0:5391;chr22:GROUPER:DEL:0:5330;chr22:GROUPER:DEL:0:5507;chr22:GROUPER:DEL:0:5024;chr22:GROUPER:DEL:0:5635;chr22:GROUPER:DEL:0:5151 CAAGTCCCCAGAGAAGGAAGAGGCCAAGTCCCCTGAGAAGGCCAAGTCCCCAGTGAAGGCAGAAGCAAAGTCCCCTGAGAAGGCCAAGTCCCCAGTGAAGGCAGAAGCA C 139 PASS NS=1;SVTYPE=DEL;SVLEN=-108;READSOURCES=(0:4);UPSTREAM=CAGCTGAGGTCAAGTCCCCGGAAAAGGCCAAGTCTCCAACGAAGGAGGAAGCAAAGTCCCCTGAGAAGGCC;DOWNSTREAM=AAGTCCCCTGAGAAGGCCAAGTCCCCAGAGAAGGAAGAGGCCAAGTCC;CONTIG=CAGCTGAGGTCAAGTCCCCGGAAAAGGCCAAGTCTCCAACGAAGGAGGAAGCAAAGTCCCCTGAGAAGGCCAAGTCCCCTGAGAAGGCCAAGTCCCCAGAGAAGGAAGAGGCCAAGTCC;CONTIG_NUM=10649;CLUSTER_NUM=10577;ensembl_gene_id=ENSG00000100285 GT ./. ./. ./. ./. 1/. 1/. ./. 1/. 1/. ./. ./. ./. ./. ./. 1/. 1/. ./. 1/. 1/. ./. ./. 1/. 1/. ./. ./. 1/. 1/. ./. 1/. 1/. 1/. 1/. 1/. 1/. ./. 1/. ./. ./. ./. ./. ./. ./. 1/. ./. 1/. 1/. ./. 1/. 1/. ./. 1/. ./. ./. ./. ./. 1/. ./. ./. 1/. ./. ./. ./. 1/. ./. ./. 1/. ./. -chr22 29885585 chr22:GROUPER:DEL:0:5578;chr22:GROUPER:DEL:0:5588;chr22:GROUPER:DEL:0:5284;chr22:GROUPER:DEL:0:5730;chr22:GROUPER:DEL:0:4909;chr22:GROUPER:DEL:0:5202;chr22:GROUPER:DEL:0:5758;chr22:GROUPER:DEL:0:5498;chr22:GROUPER:DEL:0:5216;chr22:GROUPER:DEL:0:5345;chr22:GROUPER:DEL:0:5276;chr22:GROUPER:DEL:0:5859;chr22:GROUPER:DEL:0:4589;chr22:GROUPER:DEL:0:5392;chr22:GROUPER:DEL:0:5461;chr22:GROUPER:DEL:0:4561;chr22:GROUPER:DEL:0:5825;chr22:GROUPER:DEL:0:5395;chr22:GROUPER:DEL:0:4917;chr22:GROUPER:DEL:0:4957;chr22:GROUPER:DEL:0:4764;chr22:GROUPER:DEL:0:4870;chr22:GROUPER:DEL:0:5626;chr22:GROUPER:DEL:0:5391;chr22:GROUPER:DEL:0:5330;chr22:GROUPER:DEL:0:5507;chr22:GROUPER:DEL:0:5024;chr22:GROUPER:DEL:0:5635;chr22:GROUPER:DEL:0:5151 CAAGTCCCCAGAGAAGGAAGAGGCCAAGTCCCCTGAGAAGGCCAAGTCCCCAGTGAAGGCAGAAGCAAAGTCCCCTGAGAAGGCCAAGTCCCCAGTGAAGGCAGAAGCA C 139 PASS NS=1;SVTYPE=DEL;SVLEN=-108;READSOURCES=(0:4);UPSTREAM=CAGCTGAGGTCAAGTCCCCGGAAAAGGCCAAGTCTCCAACGAAGGAGGAAGCAAAGTCCCCTGAGAAGGCC;DOWNSTREAM=AAGTCCCCTGAGAAGGCCAAGTCCCCAGAGAAGGAAGAGGCCAAGTCC;CONTIG=CAGCTGAGGTCAAGTCCCCGGAAAAGGCCAAGTCTCCAACGAAGGAGGAAGCAAAGTCCCCTGAGAAGGCCAAGTCCCCTGAGAAGGCCAAGTCCCCAGAGAAGGAAGAGGCCAAGTCC;CONTIG_NUM=10649;CLUSTER_NUM=10577;ensembl_gene_id=ENSG00000100285 GT ./. ./. ./. ./. 1/. 1/. ./. 1/. 1/. ./. ./. ./. ./. ./. 1/. 1/. ./. 1/. 1/. ./. ./. 1/. 1/. ./. ./. 1/. 1/. ./. 1/. 1/. 1/. 1/. 1/. 1/. ./. 1/. ./. ./. ./. ./. ./. ./. 1/. ./. 1/. 1/. ./. 1/. 1/. ./. 1/. ./. ./. ./. ./. 1/. ./. ./. 1/. ./. ./. ./. 1/. ./. ./. 1/. ./. -chr10 13146443 chr10:GROUPER:DEL:0:4960 TTTACTATTACAAAATTTATTTAACAAAAAGTCTAATATGAAAATGTACATGACCTA T 63 PASS NS=1;SVTYPE=DEL;SVLEN=-56;READSOURCES=(0:8);UPSTREAM=CAGCTCCCGAGTAGCTGGGACTACAGGCATGCACCACTACACCCAGCTACTTTTTTTTTTTTTTTTTT;DOWNSTREAM=ACTTTTA;CONTIG=CAGCTCCCGAGTAGCTGGGACTACAGGCATGCACCACTACACCCAGCTACTTTTTTTTTTTTTTTTTTACTTTTA;CONTIG_NUM=7987;CLUSTER_NUM=9332;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13156734 chr10:GROUPER:DEL:0:4935 AGAATATATTCTACAATTATATAATTGCATATATAATTATATAATTATATAATTATATAATTATATATACATATATATAAT A 99 PASS NS=1;SVTYPE=DEL;SVLEN=-80;READSOURCES=(0:2);UPSTREAM=TATAACGTA;DOWNSTREAM=TATATAATTATATAATTATATAATTATATAATTGTAGAATATATTCTACAATTATATAATTGTATAATATATATACACTTACATATGTATCTGTATTTTTTATAATAGATATATCTATATTTAT;CONTIG=TATAACGTATATATAATTATATAATTATATAATTATATAATTGTAGAATATATTCTACAATTATATAATTGTATAATATATATACACTTACATATGTATCTGTATTTTTTATAATAGATATATCTATATTTAT;CONTIG_NUM=7767;CLUSTER_NUM=8443;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. -chr10 13157083 chr10:GROUPER:DEL:0:5021 ATATATCTATTTTATATATTTTTATATATATTATATATATATATAAATTTATAATATAGATATATCTATATATTTATATATAGATATATCTATATTTTATATATATATTTATAGATATATCTATATTTATATATATATTTATATATAGATATATCTATATATATCTATATT A 53 PASS NS=1;SVTYPE=DEL;SVLEN=-170;READSOURCES=(0:3);UPSTREAM=TATATATATTTATAAATATAGA;DOWNSTREAM=TATATCTATATTTATATAATGAATACATATAATATATTCTATAATA;CONTIG=TATATATATTTATAAATATAGATATATCTATATTTATATAATGAATACATATAATATATTCTATAATA;CONTIG_NUM=7006;CLUSTER_NUM=6655;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13162000 chr10:GROUPER:DEL:0:5115 TGAGACGGAGTCTCGTTCTGTCACCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGTCTCCCGAGTAGCCGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTTTTTTTGTATTTTTAGTAG T 71 PASS NS=1;SVTYPE=DEL;SVLEN=-174;READSOURCES=(0:2);UPSTREAM=TTTACATTCTGGATACAAGACCCTTATTAAATATATGATCTGCAACTATTTTCTTTCTTTTTTTTTTTTTTTTTTT;DOWNSTREAM=AGACGGG;CONTIG=TTTACATTCTGGATACAAGACCCTTATTAAATATATGATCTGCAACTATTTTCTTTCTTTTTTTTTTTTTTTTTTTAGACGGG;CONTIG_NUM=8423;CLUSTER_NUM=9274;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13146443 chr10:GROUPER:DEL:0:4960 TTTACTATTACAAAATTTATTTAACAAAAAGTCTAATATGAAAATGTACATGACCTA T 63 PASS NS=1;SVTYPE=DEL;SVLEN=-56;READSOURCES=(0:8);UPSTREAM=CAGCTCCCGAGTAGCTGGGACTACAGGCATGCACCACTACACCCAGCTACTTTTTTTTTTTTTTTTTT;DOWNSTREAM=ACTTTTA;CONTIG=CAGCTCCCGAGTAGCTGGGACTACAGGCATGCACCACTACACCCAGCTACTTTTTTTTTTTTTTTTTTACTTTTA;CONTIG_NUM=7987;CLUSTER_NUM=9332;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13156734 chr10:GROUPER:DEL:0:4935 AGAATATATTCTACAATTATATAATTGCATATATAATTATATAATTATATAATTATATAATTATATATACATATATATAAT A 99 PASS NS=1;SVTYPE=DEL;SVLEN=-80;READSOURCES=(0:2);UPSTREAM=TATAACGTA;DOWNSTREAM=TATATAATTATATAATTATATAATTATATAATTGTAGAATATATTCTACAATTATATAATTGTATAATATATATACACTTACATATGTATCTGTATTTTTTATAATAGATATATCTATATTTAT;CONTIG=TATAACGTATATATAATTATATAATTATATAATTATATAATTGTAGAATATATTCTACAATTATATAATTGTATAATATATATACACTTACATATGTATCTGTATTTTTTATAATAGATATATCTATATTTAT;CONTIG_NUM=7767;CLUSTER_NUM=8443;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. -chr10 13157083 chr10:GROUPER:DEL:0:5021 ATATATCTATTTTATATATTTTTATATATATTATATATATATATAAATTTATAATATAGATATATCTATATATTTATATATAGATATATCTATATTTTATATATATATTTATAGATATATCTATATTTATATATATATTTATATATAGATATATCTATATATATCTATATT A 53 PASS NS=1;SVTYPE=DEL;SVLEN=-170;READSOURCES=(0:3);UPSTREAM=TATATATATTTATAAATATAGA;DOWNSTREAM=TATATCTATATTTATATAATGAATACATATAATATATTCTATAATA;CONTIG=TATATATATTTATAAATATAGATATATCTATATTTATATAATGAATACATATAATATATTCTATAATA;CONTIG_NUM=7006;CLUSTER_NUM=6655;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13162000 chr10:GROUPER:DEL:0:5115 TGAGACGGAGTCTCGTTCTGTCACCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGTCTCCCGAGTAGCCGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTTTTTTTGTATTTTTAGTAG T 71 PASS NS=1;SVTYPE=DEL;SVLEN=-174;READSOURCES=(0:2);UPSTREAM=TTTACATTCTGGATACAAGACCCTTATTAAATATATGATCTGCAACTATTTTCTTTCTTTTTTTTTTTTTTTTTTT;DOWNSTREAM=AGACGGG;CONTIG=TTTACATTCTGGATACAAGACCCTTATTAAATATATGATCTGCAACTATTTTCTTTCTTTTTTTTTTTTTTTTTTTAGACGGG;CONTIG_NUM=8423;CLUSTER_NUM=9274;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13146443 chr10:GROUPER:DEL:0:4960 TTTACTATTACAAAATTTATTTAACAAAAAGTCTAATATGAAAATGTACATGACCTA T 63 PASS NS=1;SVTYPE=DEL;SVLEN=-56;READSOURCES=(0:8);UPSTREAM=CAGCTCCCGAGTAGCTGGGACTACAGGCATGCACCACTACACCCAGCTACTTTTTTTTTTTTTTTTTT;DOWNSTREAM=ACTTTTA;CONTIG=CAGCTCCCGAGTAGCTGGGACTACAGGCATGCACCACTACACCCAGCTACTTTTTTTTTTTTTTTTTTACTTTTA;CONTIG_NUM=7987;CLUSTER_NUM=9332;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13156734 chr10:GROUPER:DEL:0:4935 AGAATATATTCTACAATTATATAATTGCATATATAATTATATAATTATATAATTATATAATTATATATACATATATATAAT A 99 PASS NS=1;SVTYPE=DEL;SVLEN=-80;READSOURCES=(0:2);UPSTREAM=TATAACGTA;DOWNSTREAM=TATATAATTATATAATTATATAATTATATAATTGTAGAATATATTCTACAATTATATAATTGTATAATATATATACACTTACATATGTATCTGTATTTTTTATAATAGATATATCTATATTTAT;CONTIG=TATAACGTATATATAATTATATAATTATATAATTATATAATTGTAGAATATATTCTACAATTATATAATTGTATAATATATATACACTTACATATGTATCTGTATTTTTTATAATAGATATATCTATATTTAT;CONTIG_NUM=7767;CLUSTER_NUM=8443;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. -chr10 13157083 chr10:GROUPER:DEL:0:5021 ATATATCTATTTTATATATTTTTATATATATTATATATATATATAAATTTATAATATAGATATATCTATATATTTATATATAGATATATCTATATTTTATATATATATTTATAGATATATCTATATTTATATATATATTTATATATAGATATATCTATATATATCTATATT A 53 PASS NS=1;SVTYPE=DEL;SVLEN=-170;READSOURCES=(0:3);UPSTREAM=TATATATATTTATAAATATAGA;DOWNSTREAM=TATATCTATATTTATATAATGAATACATATAATATATTCTATAATA;CONTIG=TATATATATTTATAAATATAGATATATCTATATTTATATAATGAATACATATAATATATTCTATAATA;CONTIG_NUM=7006;CLUSTER_NUM=6655;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13162000 chr10:GROUPER:DEL:0:5115 TGAGACGGAGTCTCGTTCTGTCACCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGTCTCCCGAGTAGCCGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTTTTTTTGTATTTTTAGTAG T 71 PASS NS=1;SVTYPE=DEL;SVLEN=-174;READSOURCES=(0:2);UPSTREAM=TTTACATTCTGGATACAAGACCCTTATTAAATATATGATCTGCAACTATTTTCTTTCTTTTTTTTTTTTTTTTTTT;DOWNSTREAM=AGACGGG;CONTIG=TTTACATTCTGGATACAAGACCCTTATTAAATATATGATCTGCAACTATTTTCTTTCTTTTTTTTTTTTTTTTTTTAGACGGG;CONTIG_NUM=8423;CLUSTER_NUM=9274;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13146443 chr10:GROUPER:DEL:0:4960 TTTACTATTACAAAATTTATTTAACAAAAAGTCTAATATGAAAATGTACATGACCTA T 63 PASS NS=1;SVTYPE=DEL;SVLEN=-56;READSOURCES=(0:8);UPSTREAM=CAGCTCCCGAGTAGCTGGGACTACAGGCATGCACCACTACACCCAGCTACTTTTTTTTTTTTTTTTTT;DOWNSTREAM=ACTTTTA;CONTIG=CAGCTCCCGAGTAGCTGGGACTACAGGCATGCACCACTACACCCAGCTACTTTTTTTTTTTTTTTTTTACTTTTA;CONTIG_NUM=7987;CLUSTER_NUM=9332;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13146443 chr10:GROUPER:DEL:0:4960 TTTACTATTACAAAATTTATTTAACAAAAAGTCTAATATGAAAATGTACATGACCTA T 63 PASS NS=1;SVTYPE=DEL;SVLEN=-56;READSOURCES=(0:8);UPSTREAM=CAGCTCCCGAGTAGCTGGGACTACAGGCATGCACCACTACACCCAGCTACTTTTTTTTTTTTTTTTTT;DOWNSTREAM=ACTTTTA;CONTIG=CAGCTCCCGAGTAGCTGGGACTACAGGCATGCACCACTACACCCAGCTACTTTTTTTTTTTTTTTTTTACTTTTA;CONTIG_NUM=7987;CLUSTER_NUM=9332;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13156734 chr10:GROUPER:DEL:0:4935 AGAATATATTCTACAATTATATAATTGCATATATAATTATATAATTATATAATTATATAATTATATATACATATATATAAT A 99 PASS NS=1;SVTYPE=DEL;SVLEN=-80;READSOURCES=(0:2);UPSTREAM=TATAACGTA;DOWNSTREAM=TATATAATTATATAATTATATAATTATATAATTGTAGAATATATTCTACAATTATATAATTGTATAATATATATACACTTACATATGTATCTGTATTTTTTATAATAGATATATCTATATTTAT;CONTIG=TATAACGTATATATAATTATATAATTATATAATTATATAATTGTAGAATATATTCTACAATTATATAATTGTATAATATATATACACTTACATATGTATCTGTATTTTTTATAATAGATATATCTATATTTAT;CONTIG_NUM=7767;CLUSTER_NUM=8443;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. -chr10 13157083 chr10:GROUPER:DEL:0:5021 ATATATCTATTTTATATATTTTTATATATATTATATATATATATAAATTTATAATATAGATATATCTATATATTTATATATAGATATATCTATATTTTATATATATATTTATAGATATATCTATATTTATATATATATTTATATATAGATATATCTATATATATCTATATT A 53 PASS NS=1;SVTYPE=DEL;SVLEN=-170;READSOURCES=(0:3);UPSTREAM=TATATATATTTATAAATATAGA;DOWNSTREAM=TATATCTATATTTATATAATGAATACATATAATATATTCTATAATA;CONTIG=TATATATATTTATAAATATAGATATATCTATATTTATATAATGAATACATATAATATATTCTATAATA;CONTIG_NUM=7006;CLUSTER_NUM=6655;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13146443 chr10:GROUPER:DEL:0:4960 TTTACTATTACAAAATTTATTTAACAAAAAGTCTAATATGAAAATGTACATGACCTA T 63 PASS NS=1;SVTYPE=DEL;SVLEN=-56;READSOURCES=(0:8);UPSTREAM=CAGCTCCCGAGTAGCTGGGACTACAGGCATGCACCACTACACCCAGCTACTTTTTTTTTTTTTTTTTT;DOWNSTREAM=ACTTTTA;CONTIG=CAGCTCCCGAGTAGCTGGGACTACAGGCATGCACCACTACACCCAGCTACTTTTTTTTTTTTTTTTTTACTTTTA;CONTIG_NUM=7987;CLUSTER_NUM=9332;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13156734 chr10:GROUPER:DEL:0:4935 AGAATATATTCTACAATTATATAATTGCATATATAATTATATAATTATATAATTATATAATTATATATACATATATATAAT A 99 PASS NS=1;SVTYPE=DEL;SVLEN=-80;READSOURCES=(0:2);UPSTREAM=TATAACGTA;DOWNSTREAM=TATATAATTATATAATTATATAATTATATAATTGTAGAATATATTCTACAATTATATAATTGTATAATATATATACACTTACATATGTATCTGTATTTTTTATAATAGATATATCTATATTTAT;CONTIG=TATAACGTATATATAATTATATAATTATATAATTATATAATTGTAGAATATATTCTACAATTATATAATTGTATAATATATATACACTTACATATGTATCTGTATTTTTTATAATAGATATATCTATATTTAT;CONTIG_NUM=7767;CLUSTER_NUM=8443;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. -chr10 13157083 chr10:GROUPER:DEL:0:5021 ATATATCTATTTTATATATTTTTATATATATTATATATATATATAAATTTATAATATAGATATATCTATATATTTATATATAGATATATCTATATTTTATATATATATTTATAGATATATCTATATTTATATATATATTTATATATAGATATATCTATATATATCTATATT A 53 PASS NS=1;SVTYPE=DEL;SVLEN=-170;READSOURCES=(0:3);UPSTREAM=TATATATATTTATAAATATAGA;DOWNSTREAM=TATATCTATATTTATATAATGAATACATATAATATATTCTATAATA;CONTIG=TATATATATTTATAAATATAGATATATCTATATTTATATAATGAATACATATAATATATTCTATAATA;CONTIG_NUM=7006;CLUSTER_NUM=6655;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13162000 chr10:GROUPER:DEL:0:5115 TGAGACGGAGTCTCGTTCTGTCACCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGTCTCCCGAGTAGCCGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTTTTTTTGTATTTTTAGTAG T 71 PASS NS=1;SVTYPE=DEL;SVLEN=-174;READSOURCES=(0:2);UPSTREAM=TTTACATTCTGGATACAAGACCCTTATTAAATATATGATCTGCAACTATTTTCTTTCTTTTTTTTTTTTTTTTTTT;DOWNSTREAM=AGACGGG;CONTIG=TTTACATTCTGGATACAAGACCCTTATTAAATATATGATCTGCAACTATTTTCTTTCTTTTTTTTTTTTTTTTTTTAGACGGG;CONTIG_NUM=8423;CLUSTER_NUM=9274;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13146443 chr10:GROUPER:DEL:0:4960 TTTACTATTACAAAATTTATTTAACAAAAAGTCTAATATGAAAATGTACATGACCTA T 63 PASS NS=1;SVTYPE=DEL;SVLEN=-56;READSOURCES=(0:8);UPSTREAM=CAGCTCCCGAGTAGCTGGGACTACAGGCATGCACCACTACACCCAGCTACTTTTTTTTTTTTTTTTTT;DOWNSTREAM=ACTTTTA;CONTIG=CAGCTCCCGAGTAGCTGGGACTACAGGCATGCACCACTACACCCAGCTACTTTTTTTTTTTTTTTTTTACTTTTA;CONTIG_NUM=7987;CLUSTER_NUM=9332;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13156734 chr10:GROUPER:DEL:0:4935 AGAATATATTCTACAATTATATAATTGCATATATAATTATATAATTATATAATTATATAATTATATATACATATATATAAT A 99 PASS NS=1;SVTYPE=DEL;SVLEN=-80;READSOURCES=(0:2);UPSTREAM=TATAACGTA;DOWNSTREAM=TATATAATTATATAATTATATAATTATATAATTGTAGAATATATTCTACAATTATATAATTGTATAATATATATACACTTACATATGTATCTGTATTTTTTATAATAGATATATCTATATTTAT;CONTIG=TATAACGTATATATAATTATATAATTATATAATTATATAATTGTAGAATATATTCTACAATTATATAATTGTATAATATATATACACTTACATATGTATCTGTATTTTTTATAATAGATATATCTATATTTAT;CONTIG_NUM=7767;CLUSTER_NUM=8443;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. -chr10 13157083 chr10:GROUPER:DEL:0:5021 ATATATCTATTTTATATATTTTTATATATATTATATATATATATAAATTTATAATATAGATATATCTATATATTTATATATAGATATATCTATATTTTATATATATATTTATAGATATATCTATATTTATATATATATTTATATATAGATATATCTATATATATCTATATT A 53 PASS NS=1;SVTYPE=DEL;SVLEN=-170;READSOURCES=(0:3);UPSTREAM=TATATATATTTATAAATATAGA;DOWNSTREAM=TATATCTATATTTATATAATGAATACATATAATATATTCTATAATA;CONTIG=TATATATATTTATAAATATAGATATATCTATATTTATATAATGAATACATATAATATATTCTATAATA;CONTIG_NUM=7006;CLUSTER_NUM=6655;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13162000 chr10:GROUPER:DEL:0:5115 TGAGACGGAGTCTCGTTCTGTCACCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGTCTCCCGAGTAGCCGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTTTTTTTGTATTTTTAGTAG T 71 PASS NS=1;SVTYPE=DEL;SVLEN=-174;READSOURCES=(0:2);UPSTREAM=TTTACATTCTGGATACAAGACCCTTATTAAATATATGATCTGCAACTATTTTCTTTCTTTTTTTTTTTTTTTTTTT;DOWNSTREAM=AGACGGG;CONTIG=TTTACATTCTGGATACAAGACCCTTATTAAATATATGATCTGCAACTATTTTCTTTCTTTTTTTTTTTTTTTTTTTAGACGGG;CONTIG_NUM=8423;CLUSTER_NUM=9274;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13146443 chr10:GROUPER:DEL:0:4960 TTTACTATTACAAAATTTATTTAACAAAAAGTCTAATATGAAAATGTACATGACCTA T 63 PASS NS=1;SVTYPE=DEL;SVLEN=-56;READSOURCES=(0:8);UPSTREAM=CAGCTCCCGAGTAGCTGGGACTACAGGCATGCACCACTACACCCAGCTACTTTTTTTTTTTTTTTTTT;DOWNSTREAM=ACTTTTA;CONTIG=CAGCTCCCGAGTAGCTGGGACTACAGGCATGCACCACTACACCCAGCTACTTTTTTTTTTTTTTTTTTACTTTTA;CONTIG_NUM=7987;CLUSTER_NUM=9332;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13156734 chr10:GROUPER:DEL:0:4935 AGAATATATTCTACAATTATATAATTGCATATATAATTATATAATTATATAATTATATAATTATATATACATATATATAAT A 99 PASS NS=1;SVTYPE=DEL;SVLEN=-80;READSOURCES=(0:2);UPSTREAM=TATAACGTA;DOWNSTREAM=TATATAATTATATAATTATATAATTATATAATTGTAGAATATATTCTACAATTATATAATTGTATAATATATATACACTTACATATGTATCTGTATTTTTTATAATAGATATATCTATATTTAT;CONTIG=TATAACGTATATATAATTATATAATTATATAATTATATAATTGTAGAATATATTCTACAATTATATAATTGTATAATATATATACACTTACATATGTATCTGTATTTTTTATAATAGATATATCTATATTTAT;CONTIG_NUM=7767;CLUSTER_NUM=8443;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. -chr10 13157083 chr10:GROUPER:DEL:0:5021 ATATATCTATTTTATATATTTTTATATATATTATATATATATATAAATTTATAATATAGATATATCTATATATTTATATATAGATATATCTATATTTTATATATATATTTATAGATATATCTATATTTATATATATATTTATATATAGATATATCTATATATATCTATATT A 53 PASS NS=1;SVTYPE=DEL;SVLEN=-170;READSOURCES=(0:3);UPSTREAM=TATATATATTTATAAATATAGA;DOWNSTREAM=TATATCTATATTTATATAATGAATACATATAATATATTCTATAATA;CONTIG=TATATATATTTATAAATATAGATATATCTATATTTATATAATGAATACATATAATATATTCTATAATA;CONTIG_NUM=7006;CLUSTER_NUM=6655;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13162000 chr10:GROUPER:DEL:0:5115 TGAGACGGAGTCTCGTTCTGTCACCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGTCTCCCGAGTAGCCGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTTTTTTTGTATTTTTAGTAG T 71 PASS NS=1;SVTYPE=DEL;SVLEN=-174;READSOURCES=(0:2);UPSTREAM=TTTACATTCTGGATACAAGACCCTTATTAAATATATGATCTGCAACTATTTTCTTTCTTTTTTTTTTTTTTTTTTT;DOWNSTREAM=AGACGGG;CONTIG=TTTACATTCTGGATACAAGACCCTTATTAAATATATGATCTGCAACTATTTTCTTTCTTTTTTTTTTTTTTTTTTTAGACGGG;CONTIG_NUM=8423;CLUSTER_NUM=9274;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13146443 chr10:GROUPER:DEL:0:4960 TTTACTATTACAAAATTTATTTAACAAAAAGTCTAATATGAAAATGTACATGACCTA T 63 PASS NS=1;SVTYPE=DEL;SVLEN=-56;READSOURCES=(0:8);UPSTREAM=CAGCTCCCGAGTAGCTGGGACTACAGGCATGCACCACTACACCCAGCTACTTTTTTTTTTTTTTTTTT;DOWNSTREAM=ACTTTTA;CONTIG=CAGCTCCCGAGTAGCTGGGACTACAGGCATGCACCACTACACCCAGCTACTTTTTTTTTTTTTTTTTTACTTTTA;CONTIG_NUM=7987;CLUSTER_NUM=9332;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13156734 chr10:GROUPER:DEL:0:4935 AGAATATATTCTACAATTATATAATTGCATATATAATTATATAATTATATAATTATATAATTATATATACATATATATAAT A 99 PASS NS=1;SVTYPE=DEL;SVLEN=-80;READSOURCES=(0:2);UPSTREAM=TATAACGTA;DOWNSTREAM=TATATAATTATATAATTATATAATTATATAATTGTAGAATATATTCTACAATTATATAATTGTATAATATATATACACTTACATATGTATCTGTATTTTTTATAATAGATATATCTATATTTAT;CONTIG=TATAACGTATATATAATTATATAATTATATAATTATATAATTGTAGAATATATTCTACAATTATATAATTGTATAATATATATACACTTACATATGTATCTGTATTTTTTATAATAGATATATCTATATTTAT;CONTIG_NUM=7767;CLUSTER_NUM=8443;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. -chr10 13157083 chr10:GROUPER:DEL:0:5021 ATATATCTATTTTATATATTTTTATATATATTATATATATATATAAATTTATAATATAGATATATCTATATATTTATATATAGATATATCTATATTTTATATATATATTTATAGATATATCTATATTTATATATATATTTATATATAGATATATCTATATATATCTATATT A 53 PASS NS=1;SVTYPE=DEL;SVLEN=-170;READSOURCES=(0:3);UPSTREAM=TATATATATTTATAAATATAGA;DOWNSTREAM=TATATCTATATTTATATAATGAATACATATAATATATTCTATAATA;CONTIG=TATATATATTTATAAATATAGATATATCTATATTTATATAATGAATACATATAATATATTCTATAATA;CONTIG_NUM=7006;CLUSTER_NUM=6655;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13156734 chr10:GROUPER:DEL:0:4935 AGAATATATTCTACAATTATATAATTGCATATATAATTATATAATTATATAATTATATAATTATATATACATATATATAAT A 99 PASS NS=1;SVTYPE=DEL;SVLEN=-80;READSOURCES=(0:2);UPSTREAM=TATAACGTA;DOWNSTREAM=TATATAATTATATAATTATATAATTATATAATTGTAGAATATATTCTACAATTATATAATTGTATAATATATATACACTTACATATGTATCTGTATTTTTTATAATAGATATATCTATATTTAT;CONTIG=TATAACGTATATATAATTATATAATTATATAATTATATAATTGTAGAATATATTCTACAATTATATAATTGTATAATATATATACACTTACATATGTATCTGTATTTTTTATAATAGATATATCTATATTTAT;CONTIG_NUM=7767;CLUSTER_NUM=8443;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. -chr10 13157083 chr10:GROUPER:DEL:0:5021 ATATATCTATTTTATATATTTTTATATATATTATATATATATATAAATTTATAATATAGATATATCTATATATTTATATATAGATATATCTATATTTTATATATATATTTATAGATATATCTATATTTATATATATATTTATATATAGATATATCTATATATATCTATATT A 53 PASS NS=1;SVTYPE=DEL;SVLEN=-170;READSOURCES=(0:3);UPSTREAM=TATATATATTTATAAATATAGA;DOWNSTREAM=TATATCTATATTTATATAATGAATACATATAATATATTCTATAATA;CONTIG=TATATATATTTATAAATATAGATATATCTATATTTATATAATGAATACATATAATATATTCTATAATA;CONTIG_NUM=7006;CLUSTER_NUM=6655;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr10 13162000 chr10:GROUPER:DEL:0:5115 TGAGACGGAGTCTCGTTCTGTCACCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGTCTCCCGAGTAGCCGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTTTTTTTGTATTTTTAGTAG T 71 PASS NS=1;SVTYPE=DEL;SVLEN=-174;READSOURCES=(0:2);UPSTREAM=TTTACATTCTGGATACAAGACCCTTATTAAATATATGATCTGCAACTATTTTCTTTCTTTTTTTTTTTTTTTTTTT;DOWNSTREAM=AGACGGG;CONTIG=TTTACATTCTGGATACAAGACCCTTATTAAATATATGATCTGCAACTATTTTCTTTCTTTTTTTTTTTTTTTTTTTAGACGGG;CONTIG_NUM=8423;CLUSTER_NUM=9274;ensembl_gene_id=ENSG00000123240 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr7 94931250 chr7:GROUPER:DEL:0:21227;chr7:GROUPER:DEL:0:19870;chr7:GROUPER:DEL:0:21714 ATACAAAAAATTAGCCAGGCATGGTGGCATGCGCCTGTGGTCCCAACTACTTGGGAGGCTGAGGCAGGAGAATGGTGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCAAGATTGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGATACTCTGTCAC A 59 PASS NS=1;SVTYPE=DEL;SVLEN=-158;READSOURCES=(0:4);UPSTREAM=AAAAAAAAAAAAA;DOWNSTREAM=AAAAAAAAAAAAAAAAAAAAAAAAAACAAGAATTGAGAATTATGTTGTCAGCTGAAAAAACAGT;CONTIG=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAGAATTGAGAATTATGTTGTCAGCTGAAAAAACAGT;CONTIG_NUM=55036;CLUSTER_NUM=42861;ensembl_gene_id=ENSG00000005421 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. -chr7 94983526 chr7:GROUPER:DEL:0:20091;chr7:GROUPER:DEL:0:19032 ATTAACTGGGTGTGGTGGTGCACGCCTGCAGTCCCAGCTGCTCAGGTAGGGGGATTGCTTAAGCCCAGGAGGTCAAAGCTGCAGTGAGCCATGATCATGCCATTGCACTCCAGCCTGGGTGACAGAGAGAAATCCTGTCTC A 26 PASS NS=1;SVTYPE=DEL;SVLEN=-140;READSOURCES=(0:2);UPSTREAM=AAAAAAAAAAAA;DOWNSTREAM=AAAAAAAAAAAAAAAAAAAAAAAAA;CONTIG=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA;CONTIG_NUM=50662;CLUSTER_NUM=40747;ensembl_gene_id=ENSG00000005421 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr7 95014127 chr7:GROUPER:INS:0:21388 a aCATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCC 26 PASS NS=1;SVTYPE=INS;SVLEN=68;READSOURCES=(0:2);UPSTREAM=GTGGCGATTCCTCAGGGATCTAGAACTAGAAC;DOWNSTREAM=.;CONTIG=GTGGCGATTCCTCAGGGATCTAGAACTAGAACATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCCC;CONTIG_NUM=55090;CLUSTER_NUM=43210;ensembl_gene_id=ENSG00000005421,ENSG00000105852 GT ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr7 94931250 chr7:GROUPER:DEL:0:21227;chr7:GROUPER:DEL:0:19870;chr7:GROUPER:DEL:0:21714 ATACAAAAAATTAGCCAGGCATGGTGGCATGCGCCTGTGGTCCCAACTACTTGGGAGGCTGAGGCAGGAGAATGGTGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCAAGATTGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGATACTCTGTCAC A 59 PASS NS=1;SVTYPE=DEL;SVLEN=-158;READSOURCES=(0:4);UPSTREAM=AAAAAAAAAAAAA;DOWNSTREAM=AAAAAAAAAAAAAAAAAAAAAAAAAACAAGAATTGAGAATTATGTTGTCAGCTGAAAAAACAGT;CONTIG=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAGAATTGAGAATTATGTTGTCAGCTGAAAAAACAGT;CONTIG_NUM=55036;CLUSTER_NUM=42861;ensembl_gene_id=ENSG00000005421 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. -chr7 94931250 chr7:GROUPER:DEL:0:21227;chr7:GROUPER:DEL:0:19870;chr7:GROUPER:DEL:0:21714 ATACAAAAAATTAGCCAGGCATGGTGGCATGCGCCTGTGGTCCCAACTACTTGGGAGGCTGAGGCAGGAGAATGGTGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCAAGATTGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGATACTCTGTCAC A 59 PASS NS=1;SVTYPE=DEL;SVLEN=-158;READSOURCES=(0:4);UPSTREAM=AAAAAAAAAAAAA;DOWNSTREAM=AAAAAAAAAAAAAAAAAAAAAAAAAACAAGAATTGAGAATTATGTTGTCAGCTGAAAAAACAGT;CONTIG=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAGAATTGAGAATTATGTTGTCAGCTGAAAAAACAGT;CONTIG_NUM=55036;CLUSTER_NUM=42861;ensembl_gene_id=ENSG00000005421 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. -chr7 94931250 chr7:GROUPER:DEL:0:21227;chr7:GROUPER:DEL:0:19870;chr7:GROUPER:DEL:0:21714 ATACAAAAAATTAGCCAGGCATGGTGGCATGCGCCTGTGGTCCCAACTACTTGGGAGGCTGAGGCAGGAGAATGGTGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCAAGATTGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGATACTCTGTCAC A 59 PASS NS=1;SVTYPE=DEL;SVLEN=-158;READSOURCES=(0:4);UPSTREAM=AAAAAAAAAAAAA;DOWNSTREAM=AAAAAAAAAAAAAAAAAAAAAAAAAACAAGAATTGAGAATTATGTTGTCAGCTGAAAAAACAGT;CONTIG=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAGAATTGAGAATTATGTTGTCAGCTGAAAAAACAGT;CONTIG_NUM=55036;CLUSTER_NUM=42861;ensembl_gene_id=ENSG00000005421 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. -chr7 94931250 chr7:GROUPER:DEL:0:21227;chr7:GROUPER:DEL:0:19870;chr7:GROUPER:DEL:0:21714 ATACAAAAAATTAGCCAGGCATGGTGGCATGCGCCTGTGGTCCCAACTACTTGGGAGGCTGAGGCAGGAGAATGGTGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCAAGATTGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGATACTCTGTCAC A 59 PASS NS=1;SVTYPE=DEL;SVLEN=-158;READSOURCES=(0:4);UPSTREAM=AAAAAAAAAAAAA;DOWNSTREAM=AAAAAAAAAAAAAAAAAAAAAAAAAACAAGAATTGAGAATTATGTTGTCAGCTGAAAAAACAGT;CONTIG=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAGAATTGAGAATTATGTTGTCAGCTGAAAAAACAGT;CONTIG_NUM=55036;CLUSTER_NUM=42861;ensembl_gene_id=ENSG00000005421 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. -chr7 94983526 chr7:GROUPER:DEL:0:20091;chr7:GROUPER:DEL:0:19032 ATTAACTGGGTGTGGTGGTGCACGCCTGCAGTCCCAGCTGCTCAGGTAGGGGGATTGCTTAAGCCCAGGAGGTCAAAGCTGCAGTGAGCCATGATCATGCCATTGCACTCCAGCCTGGGTGACAGAGAGAAATCCTGTCTC A 26 PASS NS=1;SVTYPE=DEL;SVLEN=-140;READSOURCES=(0:2);UPSTREAM=AAAAAAAAAAAA;DOWNSTREAM=AAAAAAAAAAAAAAAAAAAAAAAAA;CONTIG=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA;CONTIG_NUM=50662;CLUSTER_NUM=40747;ensembl_gene_id=ENSG00000005421 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr7 95014127 chr7:GROUPER:INS:0:21388 a aCATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCC 26 PASS NS=1;SVTYPE=INS;SVLEN=68;READSOURCES=(0:2);UPSTREAM=GTGGCGATTCCTCAGGGATCTAGAACTAGAAC;DOWNSTREAM=.;CONTIG=GTGGCGATTCCTCAGGGATCTAGAACTAGAACATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCCC;CONTIG_NUM=55090;CLUSTER_NUM=43210;ensembl_gene_id=ENSG00000005421,ENSG00000105852 GT ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr7 95014127 chr7:GROUPER:INS:0:21388 a aCATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCC 26 PASS NS=1;SVTYPE=INS;SVLEN=68;READSOURCES=(0:2);UPSTREAM=GTGGCGATTCCTCAGGGATCTAGAACTAGAAC;DOWNSTREAM=.;CONTIG=GTGGCGATTCCTCAGGGATCTAGAACTAGAACATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCCC;CONTIG_NUM=55090;CLUSTER_NUM=43210;ensembl_gene_id=ENSG00000005421,ENSG00000105852 GT ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr7 95014127 chr7:GROUPER:INS:0:21388 a aCATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCC 26 PASS NS=1;SVTYPE=INS;SVLEN=68;READSOURCES=(0:2);UPSTREAM=GTGGCGATTCCTCAGGGATCTAGAACTAGAAC;DOWNSTREAM=.;CONTIG=GTGGCGATTCCTCAGGGATCTAGAACTAGAACATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCCC;CONTIG_NUM=55090;CLUSTER_NUM=43210;ensembl_gene_id=ENSG00000005421,ENSG00000105852 GT ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr7 95014127 chr7:GROUPER:INS:0:21388 a aCATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCC 26 PASS NS=1;SVTYPE=INS;SVLEN=68;READSOURCES=(0:2);UPSTREAM=GTGGCGATTCCTCAGGGATCTAGAACTAGAAC;DOWNSTREAM=.;CONTIG=GTGGCGATTCCTCAGGGATCTAGAACTAGAACATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCCC;CONTIG_NUM=55090;CLUSTER_NUM=43210;ensembl_gene_id=ENSG00000005421,ENSG00000105852 GT ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr7 95014127 chr7:GROUPER:INS:0:21388 a aCATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCC 26 PASS NS=1;SVTYPE=INS;SVLEN=68;READSOURCES=(0:2);UPSTREAM=GTGGCGATTCCTCAGGGATCTAGAACTAGAAC;DOWNSTREAM=.;CONTIG=GTGGCGATTCCTCAGGGATCTAGAACTAGAACATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCCC;CONTIG_NUM=55090;CLUSTER_NUM=43210;ensembl_gene_id=ENSG00000005421,ENSG00000105852 GT ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr7 95014127 chr7:GROUPER:INS:0:21388 a aCATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCC 26 PASS NS=1;SVTYPE=INS;SVLEN=68;READSOURCES=(0:2);UPSTREAM=GTGGCGATTCCTCAGGGATCTAGAACTAGAAC;DOWNSTREAM=.;CONTIG=GTGGCGATTCCTCAGGGATCTAGAACTAGAACATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCCC;CONTIG_NUM=55090;CLUSTER_NUM=43210;ensembl_gene_id=ENSG00000005421,ENSG00000105852 GT ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr7 95014127 chr7:GROUPER:INS:0:21388 a aCATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCC 26 PASS NS=1;SVTYPE=INS;SVLEN=68;READSOURCES=(0:2);UPSTREAM=GTGGCGATTCCTCAGGGATCTAGAACTAGAAC;DOWNSTREAM=.;CONTIG=GTGGCGATTCCTCAGGGATCTAGAACTAGAACATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCCC;CONTIG_NUM=55090;CLUSTER_NUM=43210;ensembl_gene_id=ENSG00000005421,ENSG00000105852 GT ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr7 95014127 chr7:GROUPER:INS:0:21388 a aCATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCC 26 PASS NS=1;SVTYPE=INS;SVLEN=68;READSOURCES=(0:2);UPSTREAM=GTGGCGATTCCTCAGGGATCTAGAACTAGAAC;DOWNSTREAM=.;CONTIG=GTGGCGATTCCTCAGGGATCTAGAACTAGAACATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCCC;CONTIG_NUM=55090;CLUSTER_NUM=43210;ensembl_gene_id=ENSG00000005421,ENSG00000105852 GT ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr7 95014127 chr7:GROUPER:INS:0:21388 a aCATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCC 26 PASS NS=1;SVTYPE=INS;SVLEN=68;READSOURCES=(0:2);UPSTREAM=GTGGCGATTCCTCAGGGATCTAGAACTAGAAC;DOWNSTREAM=.;CONTIG=GTGGCGATTCCTCAGGGATCTAGAACTAGAACATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCCC;CONTIG_NUM=55090;CLUSTER_NUM=43210;ensembl_gene_id=ENSG00000005421,ENSG00000105852 GT ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr7 95014127 chr7:GROUPER:INS:0:21388 a aCATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCC 26 PASS NS=1;SVTYPE=INS;SVLEN=68;READSOURCES=(0:2);UPSTREAM=GTGGCGATTCCTCAGGGATCTAGAACTAGAAC;DOWNSTREAM=.;CONTIG=GTGGCGATTCCTCAGGGATCTAGAACTAGAACATTTGTTTTTATAGAGCAGTTTTGAAAATCTCTTTTTGTGGAGTCTGGAAGTGGATATTTGGTTCCCC;CONTIG_NUM=55090;CLUSTER_NUM=43210;ensembl_gene_id=ENSG00000005421,ENSG00000105852 GT ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr9 135186642 chr9:GROUPER:INS:0:9971;chr9:GROUPER:INS:0:9507;chr9:GROUPER:INS:0:10283;chr9:GROUPER:INS:0:9566;chr9:GROUPER:INS:0:10334;chr9:GROUPER:INS:0:9888;chr9:GROUPER:INS:0:9631;chr9:GROUPER:INS:0:8925;chr9:GROUPER:INS:0:8928;chr9:GROUPER:INS:0:8685;chr9:GROUPER:INS:0:10776;chr9:GROUPER:INS:0:9668;chr9:GROUPER:INS:0:10189;chr9:GROUPER:INS:0:9217;chr9:GROUPER:INS:0:8834;chr9:GROUPER:INS:0:9096;chr9:GROUPER:INS:0:10104;chr9:GROUPER:INS:0:9022;chr9:GROUPER:INS:0:10015;chr9:GROUPER:INS:0:10298;chr9:GROUPER:INS:0:8621;chr9:GROUPER:INS:0:9793;chr9:GROUPER:INS:0:10170;chr9:GROUPER:INS:0:8792;chr9:GROUPER:INS:0:9435;chr9:GROUPER:INS:0:9874;chr9:GROUPER:INS:0:9711;chr9:GROUPER:INS:0:8946;chr9:GROUPER:INS:0:9498;chr9:GROUPER:INS:0:8397;chr9:GROUPER:INS:0:8624;chr9:GROUPER:INS:0:9996;chr9:GROUPER:INS:0:10307;chr9:GROUPER:INS:0:10031;chr9:GROUPER:INS:0:9693;chr9:GROUPER:INS:0:9970;chr9:GROUPER:INS:0:10379;chr9:GROUPER:INS:0:9149;chr9:GROUPER:INS:0:9165;chr9:GROUPER:INS:0:9440;chr9:GROUPER:INS:0:9798;chr9:GROUPER:INS:0:10079;chr9:GROUPER:INS:0:9901;chr9:GROUPER:INS:0:9620;chr9:GROUPER:INS:0:10601 C CTGAGCCCGGCCTTCTCTTGACGTTTAAACTATGAAGTCAGTCCAGAGAAA 39 PASS NS=1;SVTYPE=INS;SVLEN=50;READSOURCES=(0:2);UPSTREAM=CCCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATGACAGGCGTGAGCCAC;DOWNSTREAM=.;CONTIG=CCCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATGACAGGCGTGAGCCACTGAGCCCGGCCTTCTCTTGACGTTTAAACTATGAAGTCAGTCCAGAGAAA;CONTIG_NUM=16137;CLUSTER_NUM=19547;ensembl_gene_id=ENSG00000107290 GT ./. 1/. ./. ./. 1/. ./. 1/. ./. 1/. 1/. ./. ./. 1/. 1/. 1/. 1/. 1/. 1/. 1/. ./. ./. 1/. 1/. ./. 1/. 1/. 1/. ./. 1/. 1/. 1/. 1/. 1/. 1/. ./. 1/. ./. 1/. 1/. 1/. ./. 1/. 1/. ./. 1/. 1/. ./. 1/. 1/. ./. 1/. ./. ./. 1/. 1/. 1/. 1/. ./. ./. 1/. 1/. 1/. 1/. 1/. 1/. 1/. 1/. -chr9 135198111 chr9:GROUPER:DEL:0:10781;chr9:GROUPER:DEL:0:9671;chr9:GROUPER:DEL:0:10118;chr9:GROUPER:DEL:0:10192;chr9:GROUPER:DEL:0:10302;chr9:GROUPER:DEL:0:8624;chr9:GROUPER:DEL:0:9440;chr9:GROUPER:DEL:0:8630;chr9:GROUPER:DEL:0:9999;chr9:GROUPER:DEL:0:10034;chr9:GROUPER:DEL:0:9696;chr9:GROUPER:DEL:0:9151;chr9:GROUPER:DEL:0:10081 ACCACCTGAAAAAAGGAATTAACAGAAAGGACTATAAACACTAAAATGAACAGGAAAAACCAACTGGGGAAACACGAACCATGCAAAAAGAGAAAAACTTTTAGCTAACTTTAAAATTATC A 80 PASS NS=1;SVTYPE=DEL;SVLEN=-120;READSOURCES=(0:32);UPSTREAM=ATCATTA;DOWNSTREAM=ATAAACTTTAGCTAATAAAAAATACCACATCCATGAAATAGAATAAAGGA;CONTIG=ATCATTAATAAACTTTAGCTAATAAAAAATACCACATCCATGAAATAGAATAAAGGA;CONTIG_NUM=17339;CLUSTER_NUM=20249;ensembl_gene_id=ENSG00000107290 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. 1/. ./. 1/. 1/. ./. ./. ./. ./. ./. ./. ./. ./. 1/. 1/. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. 1/. ./. 1/. ./. ./. 1/. ./. ./. 1/. ./. ./. 1/. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. -chr9 135186642 chr9:GROUPER:INS:0:9971;chr9:GROUPER:INS:0:9507;chr9:GROUPER:INS:0:10283;chr9:GROUPER:INS:0:9566;chr9:GROUPER:INS:0:10334;chr9:GROUPER:INS:0:9888;chr9:GROUPER:INS:0:9631;chr9:GROUPER:INS:0:8925;chr9:GROUPER:INS:0:8928;chr9:GROUPER:INS:0:8685;chr9:GROUPER:INS:0:10776;chr9:GROUPER:INS:0:9668;chr9:GROUPER:INS:0:10189;chr9:GROUPER:INS:0:9217;chr9:GROUPER:INS:0:8834;chr9:GROUPER:INS:0:9096;chr9:GROUPER:INS:0:10104;chr9:GROUPER:INS:0:9022;chr9:GROUPER:INS:0:10015;chr9:GROUPER:INS:0:10298;chr9:GROUPER:INS:0:8621;chr9:GROUPER:INS:0:9793;chr9:GROUPER:INS:0:10170;chr9:GROUPER:INS:0:8792;chr9:GROUPER:INS:0:9435;chr9:GROUPER:INS:0:9874;chr9:GROUPER:INS:0:9711;chr9:GROUPER:INS:0:8946;chr9:GROUPER:INS:0:9498;chr9:GROUPER:INS:0:8397;chr9:GROUPER:INS:0:8624;chr9:GROUPER:INS:0:9996;chr9:GROUPER:INS:0:10307;chr9:GROUPER:INS:0:10031;chr9:GROUPER:INS:0:9693;chr9:GROUPER:INS:0:9970;chr9:GROUPER:INS:0:10379;chr9:GROUPER:INS:0:9149;chr9:GROUPER:INS:0:9165;chr9:GROUPER:INS:0:9440;chr9:GROUPER:INS:0:9798;chr9:GROUPER:INS:0:10079;chr9:GROUPER:INS:0:9901;chr9:GROUPER:INS:0:9620;chr9:GROUPER:INS:0:10601 C CTGAGCCCGGCCTTCTCTTGACGTTTAAACTATGAAGTCAGTCCAGAGAAA 39 PASS NS=1;SVTYPE=INS;SVLEN=50;READSOURCES=(0:2);UPSTREAM=CCCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATGACAGGCGTGAGCCAC;DOWNSTREAM=.;CONTIG=CCCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATGACAGGCGTGAGCCACTGAGCCCGGCCTTCTCTTGACGTTTAAACTATGAAGTCAGTCCAGAGAAA;CONTIG_NUM=16137;CLUSTER_NUM=19547;ensembl_gene_id=ENSG00000107290 GT ./. 1/. ./. ./. 1/. ./. 1/. ./. 1/. 1/. ./. ./. 1/. 1/. 1/. 1/. 1/. 1/. 1/. ./. ./. 1/. 1/. ./. 1/. 1/. 1/. ./. 1/. 1/. 1/. 1/. 1/. 1/. ./. 1/. ./. 1/. 1/. 1/. ./. 1/. 1/. ./. 1/. 1/. ./. 1/. 1/. ./. 1/. ./. ./. 1/. 1/. 1/. 1/. ./. ./. 1/. 1/. 1/. 1/. 1/. 1/. 1/. 1/. -chr9 135186642 chr9:GROUPER:INS:0:9971;chr9:GROUPER:INS:0:9507;chr9:GROUPER:INS:0:10283;chr9:GROUPER:INS:0:9566;chr9:GROUPER:INS:0:10334;chr9:GROUPER:INS:0:9888;chr9:GROUPER:INS:0:9631;chr9:GROUPER:INS:0:8925;chr9:GROUPER:INS:0:8928;chr9:GROUPER:INS:0:8685;chr9:GROUPER:INS:0:10776;chr9:GROUPER:INS:0:9668;chr9:GROUPER:INS:0:10189;chr9:GROUPER:INS:0:9217;chr9:GROUPER:INS:0:8834;chr9:GROUPER:INS:0:9096;chr9:GROUPER:INS:0:10104;chr9:GROUPER:INS:0:9022;chr9:GROUPER:INS:0:10015;chr9:GROUPER:INS:0:10298;chr9:GROUPER:INS:0:8621;chr9:GROUPER:INS:0:9793;chr9:GROUPER:INS:0:10170;chr9:GROUPER:INS:0:8792;chr9:GROUPER:INS:0:9435;chr9:GROUPER:INS:0:9874;chr9:GROUPER:INS:0:9711;chr9:GROUPER:INS:0:8946;chr9:GROUPER:INS:0:9498;chr9:GROUPER:INS:0:8397;chr9:GROUPER:INS:0:8624;chr9:GROUPER:INS:0:9996;chr9:GROUPER:INS:0:10307;chr9:GROUPER:INS:0:10031;chr9:GROUPER:INS:0:9693;chr9:GROUPER:INS:0:9970;chr9:GROUPER:INS:0:10379;chr9:GROUPER:INS:0:9149;chr9:GROUPER:INS:0:9165;chr9:GROUPER:INS:0:9440;chr9:GROUPER:INS:0:9798;chr9:GROUPER:INS:0:10079;chr9:GROUPER:INS:0:9901;chr9:GROUPER:INS:0:9620;chr9:GROUPER:INS:0:10601 C CTGAGCCCGGCCTTCTCTTGACGTTTAAACTATGAAGTCAGTCCAGAGAAA 39 PASS NS=1;SVTYPE=INS;SVLEN=50;READSOURCES=(0:2);UPSTREAM=CCCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATGACAGGCGTGAGCCAC;DOWNSTREAM=.;CONTIG=CCCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATGACAGGCGTGAGCCACTGAGCCCGGCCTTCTCTTGACGTTTAAACTATGAAGTCAGTCCAGAGAAA;CONTIG_NUM=16137;CLUSTER_NUM=19547;ensembl_gene_id=ENSG00000107290 GT ./. 1/. ./. ./. 1/. ./. 1/. ./. 1/. 1/. ./. ./. 1/. 1/. 1/. 1/. 1/. 1/. 1/. ./. ./. 1/. 1/. ./. 1/. 1/. 1/. ./. 1/. 1/. 1/. 1/. 1/. 1/. ./. 1/. ./. 1/. 1/. 1/. ./. 1/. 1/. ./. 1/. 1/. ./. 1/. 1/. ./. 1/. ./. ./. 1/. 1/. 1/. 1/. ./. ./. 1/. 1/. 1/. 1/. 1/. 1/. 1/. 1/. -chr9 135198111 chr9:GROUPER:DEL:0:10781;chr9:GROUPER:DEL:0:9671;chr9:GROUPER:DEL:0:10118;chr9:GROUPER:DEL:0:10192;chr9:GROUPER:DEL:0:10302;chr9:GROUPER:DEL:0:8624;chr9:GROUPER:DEL:0:9440;chr9:GROUPER:DEL:0:8630;chr9:GROUPER:DEL:0:9999;chr9:GROUPER:DEL:0:10034;chr9:GROUPER:DEL:0:9696;chr9:GROUPER:DEL:0:9151;chr9:GROUPER:DEL:0:10081 ACCACCTGAAAAAAGGAATTAACAGAAAGGACTATAAACACTAAAATGAACAGGAAAAACCAACTGGGGAAACACGAACCATGCAAAAAGAGAAAAACTTTTAGCTAACTTTAAAATTATC A 80 PASS NS=1;SVTYPE=DEL;SVLEN=-120;READSOURCES=(0:32);UPSTREAM=ATCATTA;DOWNSTREAM=ATAAACTTTAGCTAATAAAAAATACCACATCCATGAAATAGAATAAAGGA;CONTIG=ATCATTAATAAACTTTAGCTAATAAAAAATACCACATCCATGAAATAGAATAAAGGA;CONTIG_NUM=17339;CLUSTER_NUM=20249;ensembl_gene_id=ENSG00000107290 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. 1/. ./. 1/. 1/. ./. ./. ./. ./. ./. ./. ./. ./. 1/. 1/. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. 1/. ./. 1/. ./. ./. 1/. ./. ./. 1/. ./. ./. 1/. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. -chr9 135186642 chr9:GROUPER:INS:0:9971;chr9:GROUPER:INS:0:9507;chr9:GROUPER:INS:0:10283;chr9:GROUPER:INS:0:9566;chr9:GROUPER:INS:0:10334;chr9:GROUPER:INS:0:9888;chr9:GROUPER:INS:0:9631;chr9:GROUPER:INS:0:8925;chr9:GROUPER:INS:0:8928;chr9:GROUPER:INS:0:8685;chr9:GROUPER:INS:0:10776;chr9:GROUPER:INS:0:9668;chr9:GROUPER:INS:0:10189;chr9:GROUPER:INS:0:9217;chr9:GROUPER:INS:0:8834;chr9:GROUPER:INS:0:9096;chr9:GROUPER:INS:0:10104;chr9:GROUPER:INS:0:9022;chr9:GROUPER:INS:0:10015;chr9:GROUPER:INS:0:10298;chr9:GROUPER:INS:0:8621;chr9:GROUPER:INS:0:9793;chr9:GROUPER:INS:0:10170;chr9:GROUPER:INS:0:8792;chr9:GROUPER:INS:0:9435;chr9:GROUPER:INS:0:9874;chr9:GROUPER:INS:0:9711;chr9:GROUPER:INS:0:8946;chr9:GROUPER:INS:0:9498;chr9:GROUPER:INS:0:8397;chr9:GROUPER:INS:0:8624;chr9:GROUPER:INS:0:9996;chr9:GROUPER:INS:0:10307;chr9:GROUPER:INS:0:10031;chr9:GROUPER:INS:0:9693;chr9:GROUPER:INS:0:9970;chr9:GROUPER:INS:0:10379;chr9:GROUPER:INS:0:9149;chr9:GROUPER:INS:0:9165;chr9:GROUPER:INS:0:9440;chr9:GROUPER:INS:0:9798;chr9:GROUPER:INS:0:10079;chr9:GROUPER:INS:0:9901;chr9:GROUPER:INS:0:9620;chr9:GROUPER:INS:0:10601 C CTGAGCCCGGCCTTCTCTTGACGTTTAAACTATGAAGTCAGTCCAGAGAAA 39 PASS NS=1;SVTYPE=INS;SVLEN=50;READSOURCES=(0:2);UPSTREAM=CCCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATGACAGGCGTGAGCCAC;DOWNSTREAM=.;CONTIG=CCCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATGACAGGCGTGAGCCACTGAGCCCGGCCTTCTCTTGACGTTTAAACTATGAAGTCAGTCCAGAGAAA;CONTIG_NUM=16137;CLUSTER_NUM=19547;ensembl_gene_id=ENSG00000107290 GT ./. 1/. ./. ./. 1/. ./. 1/. ./. 1/. 1/. ./. ./. 1/. 1/. 1/. 1/. 1/. 1/. 1/. ./. ./. 1/. 1/. ./. 1/. 1/. 1/. ./. 1/. 1/. 1/. 1/. 1/. 1/. ./. 1/. ./. 1/. 1/. 1/. ./. 1/. 1/. ./. 1/. 1/. ./. 1/. 1/. ./. 1/. ./. ./. 1/. 1/. 1/. 1/. ./. ./. 1/. 1/. 1/. 1/. 1/. 1/. 1/. 1/. -chr9 135198111 chr9:GROUPER:DEL:0:10781;chr9:GROUPER:DEL:0:9671;chr9:GROUPER:DEL:0:10118;chr9:GROUPER:DEL:0:10192;chr9:GROUPER:DEL:0:10302;chr9:GROUPER:DEL:0:8624;chr9:GROUPER:DEL:0:9440;chr9:GROUPER:DEL:0:8630;chr9:GROUPER:DEL:0:9999;chr9:GROUPER:DEL:0:10034;chr9:GROUPER:DEL:0:9696;chr9:GROUPER:DEL:0:9151;chr9:GROUPER:DEL:0:10081 ACCACCTGAAAAAAGGAATTAACAGAAAGGACTATAAACACTAAAATGAACAGGAAAAACCAACTGGGGAAACACGAACCATGCAAAAAGAGAAAAACTTTTAGCTAACTTTAAAATTATC A 80 PASS NS=1;SVTYPE=DEL;SVLEN=-120;READSOURCES=(0:32);UPSTREAM=ATCATTA;DOWNSTREAM=ATAAACTTTAGCTAATAAAAAATACCACATCCATGAAATAGAATAAAGGA;CONTIG=ATCATTAATAAACTTTAGCTAATAAAAAATACCACATCCATGAAATAGAATAAAGGA;CONTIG_NUM=17339;CLUSTER_NUM=20249;ensembl_gene_id=ENSG00000107290 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. 1/. ./. 1/. 1/. ./. ./. ./. ./. ./. ./. ./. ./. 1/. 1/. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. 1/. ./. 1/. ./. ./. 1/. ./. ./. 1/. ./. ./. 1/. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. -chr1 11075541 chr1:GROUPER:DEL:0:3560;chr1:GROUPER:DEL:0:3767 AAAAAAAATTTTTTAAATGTCATTTAATTTATCTCCCCAGGCTGGACATGGTGGCTCACATCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCCGGGAGGCAGAGGTTGCAGAGAGGGGAGATTGCGCCACTGCACTCCAGCCTAGGTGACAGAATGAGACTCCGTCTC A 91 PASS NS=1;SVTYPE=DEL;SVLEN=-185;READSOURCES=(0:22);UPSTREAM=CCGTCTCA;DOWNSTREAM=AAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG=CCGTCTCAAAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG_NUM=7310;CLUSTER_NUM=7538;ensembl_gene_id=ENSG00000120948 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr1 11075541 chr1:GROUPER:DEL:0:3560;chr1:GROUPER:DEL:0:3767 AAAAAAAATTTTTTAAATGTCATTTAATTTATCTCCCCAGGCTGGACATGGTGGCTCACATCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCCGGGAGGCAGAGGTTGCAGAGAGGGGAGATTGCGCCACTGCACTCCAGCCTAGGTGACAGAATGAGACTCCGTCTC A 91 PASS NS=1;SVTYPE=DEL;SVLEN=-185;READSOURCES=(0:22);UPSTREAM=CCGTCTCA;DOWNSTREAM=AAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG=CCGTCTCAAAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG_NUM=7310;CLUSTER_NUM=7538;ensembl_gene_id=ENSG00000120948 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr1 11075541 chr1:GROUPER:DEL:0:3560;chr1:GROUPER:DEL:0:3767 AAAAAAAATTTTTTAAATGTCATTTAATTTATCTCCCCAGGCTGGACATGGTGGCTCACATCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCCGGGAGGCAGAGGTTGCAGAGAGGGGAGATTGCGCCACTGCACTCCAGCCTAGGTGACAGAATGAGACTCCGTCTC A 91 PASS NS=1;SVTYPE=DEL;SVLEN=-185;READSOURCES=(0:22);UPSTREAM=CCGTCTCA;DOWNSTREAM=AAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG=CCGTCTCAAAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG_NUM=7310;CLUSTER_NUM=7538;ensembl_gene_id=ENSG00000120948 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr1 11075541 chr1:GROUPER:DEL:0:3560;chr1:GROUPER:DEL:0:3767 AAAAAAAATTTTTTAAATGTCATTTAATTTATCTCCCCAGGCTGGACATGGTGGCTCACATCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCCGGGAGGCAGAGGTTGCAGAGAGGGGAGATTGCGCCACTGCACTCCAGCCTAGGTGACAGAATGAGACTCCGTCTC A 91 PASS NS=1;SVTYPE=DEL;SVLEN=-185;READSOURCES=(0:22);UPSTREAM=CCGTCTCA;DOWNSTREAM=AAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG=CCGTCTCAAAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG_NUM=7310;CLUSTER_NUM=7538;ensembl_gene_id=ENSG00000120948 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr1 11075541 chr1:GROUPER:DEL:0:3560;chr1:GROUPER:DEL:0:3767 AAAAAAAATTTTTTAAATGTCATTTAATTTATCTCCCCAGGCTGGACATGGTGGCTCACATCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCCGGGAGGCAGAGGTTGCAGAGAGGGGAGATTGCGCCACTGCACTCCAGCCTAGGTGACAGAATGAGACTCCGTCTC A 91 PASS NS=1;SVTYPE=DEL;SVLEN=-185;READSOURCES=(0:22);UPSTREAM=CCGTCTCA;DOWNSTREAM=AAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG=CCGTCTCAAAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG_NUM=7310;CLUSTER_NUM=7538;ensembl_gene_id=ENSG00000120948 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr1 11075541 chr1:GROUPER:DEL:0:3560;chr1:GROUPER:DEL:0:3767 AAAAAAAATTTTTTAAATGTCATTTAATTTATCTCCCCAGGCTGGACATGGTGGCTCACATCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCCGGGAGGCAGAGGTTGCAGAGAGGGGAGATTGCGCCACTGCACTCCAGCCTAGGTGACAGAATGAGACTCCGTCTC A 91 PASS NS=1;SVTYPE=DEL;SVLEN=-185;READSOURCES=(0:22);UPSTREAM=CCGTCTCA;DOWNSTREAM=AAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG=CCGTCTCAAAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG_NUM=7310;CLUSTER_NUM=7538;ensembl_gene_id=ENSG00000120948 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr1 11075541 chr1:GROUPER:DEL:0:3560;chr1:GROUPER:DEL:0:3767 AAAAAAAATTTTTTAAATGTCATTTAATTTATCTCCCCAGGCTGGACATGGTGGCTCACATCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCCGGGAGGCAGAGGTTGCAGAGAGGGGAGATTGCGCCACTGCACTCCAGCCTAGGTGACAGAATGAGACTCCGTCTC A 91 PASS NS=1;SVTYPE=DEL;SVLEN=-185;READSOURCES=(0:22);UPSTREAM=CCGTCTCA;DOWNSTREAM=AAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG=CCGTCTCAAAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG_NUM=7310;CLUSTER_NUM=7538;ensembl_gene_id=ENSG00000120948 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr1 11075541 chr1:GROUPER:DEL:0:3560;chr1:GROUPER:DEL:0:3767 AAAAAAAATTTTTTAAATGTCATTTAATTTATCTCCCCAGGCTGGACATGGTGGCTCACATCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCCGGGAGGCAGAGGTTGCAGAGAGGGGAGATTGCGCCACTGCACTCCAGCCTAGGTGACAGAATGAGACTCCGTCTC A 91 PASS NS=1;SVTYPE=DEL;SVLEN=-185;READSOURCES=(0:22);UPSTREAM=CCGTCTCA;DOWNSTREAM=AAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG=CCGTCTCAAAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG_NUM=7310;CLUSTER_NUM=7538;ensembl_gene_id=ENSG00000120948 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr1 11075541 chr1:GROUPER:DEL:0:3560;chr1:GROUPER:DEL:0:3767 AAAAAAAATTTTTTAAATGTCATTTAATTTATCTCCCCAGGCTGGACATGGTGGCTCACATCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCCGGGAGGCAGAGGTTGCAGAGAGGGGAGATTGCGCCACTGCACTCCAGCCTAGGTGACAGAATGAGACTCCGTCTC A 91 PASS NS=1;SVTYPE=DEL;SVLEN=-185;READSOURCES=(0:22);UPSTREAM=CCGTCTCA;DOWNSTREAM=AAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG=CCGTCTCAAAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG_NUM=7310;CLUSTER_NUM=7538;ensembl_gene_id=ENSG00000120948 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr1 11075541 chr1:GROUPER:DEL:0:3560;chr1:GROUPER:DEL:0:3767 AAAAAAAATTTTTTAAATGTCATTTAATTTATCTCCCCAGGCTGGACATGGTGGCTCACATCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCCGGGAGGCAGAGGTTGCAGAGAGGGGAGATTGCGCCACTGCACTCCAGCCTAGGTGACAGAATGAGACTCCGTCTC A 91 PASS NS=1;SVTYPE=DEL;SVLEN=-185;READSOURCES=(0:22);UPSTREAM=CCGTCTCA;DOWNSTREAM=AAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG=CCGTCTCAAAAAAAAAAAAATTATCTCCCCTTCTCTTCTAAATAACCTAAGGTTGAGGTTATTTGGGGGGTTTTTTTGTTGTTGTTTGTTTGTTTGTTTTTTG;CONTIG_NUM=7310;CLUSTER_NUM=7538;ensembl_gene_id=ENSG00000120948 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56990993 chr20:GROUPER:INS:0:2164 A ATGGAGAAATTCTCATGGAGTATTTCATCTGTGAAGGCGTCACTGCTCGTGGAATGAGAATAGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAG 1 PASS NS=1;SVTYPE=INS;SVLEN=113;READSOURCES=(0:4);UPSTREAM=AGCAAAT;DOWNSTREAM=.;CONTIG=AGCAAATGGAGAAATTCTCATGGAGTATTTCATCTGTGAAGGCGTCACTGCTCGTGGAATGAGAATAGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGT;CONTIG_NUM=3355;CLUSTER_NUM=4093;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991105 chr20:GROUPER:INS:0:2272 T TGGGGAACTGACTTAGAGTGTAGTGATAGGGTTGTTTGTGATAGGCAGGTAAGCAAATGGAGAAATTCTCATGGAGTATTTCATCTGTGAAGGCGTCACTGCTCGTGGAATGAGAATAGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAG 2 PASS NS=1;SVTYPE=INS;SVLEN=193;READSOURCES=(0:8);UPSTREAM=TTTTCAGT;DOWNSTREAM=.;CONTIG=TTTTCAGTGGGGAACTGACTTAGAGTGTAGTGATAGGGTTGTTTGTGATAGGCAGGTAAGCAAATGGAGAAATTCTCATGGAGTATTTCATCTGTGAAGGCGTCACTGCTCGTGGAATGAGAATAGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAG;CONTIG_NUM=3531;CLUSTER_NUM=4250;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991110 chr20:GROUPER:INS:0:2162 T TCAGTTCTGCTGTAATGCATTCCTGGAGAATCACCACACTATACTGAATAGCTTGGTAAAAACCACAGCGCTTATGAGGGAAGTGCGGTTAGGAGCACAGCACTCCAAGACTTTGTTGGTGACACGTGCACAAAGATAGGGCGCTGG 2 PASS NS=1;SVTYPE=INS;SVLEN=146;READSOURCES=(0:13);UPSTREAM=AGTATAGT;DOWNSTREAM=.;CONTIG=AGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAGAATCACCACACTATACTGAATAGCTTGGTAAAAACCACAGCGCTTATGAGGGAAGTGCGGTTAGGAGCACAGCACTCCAAGACTTTGTTGGTGACACGTGCACAAAGATAGGGCGCTGG;CONTIG_NUM=3353;CLUSTER_NUM=4093;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991372 chr20:GROUPER:INS:0:2274 T TGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAGAATCACCACACTATACTGAATAGCTTGGTAAAAACCACAGCGCTTATGAGGGAAGTGCGGTTAGGAGCACAGCACTCCAAGACTTTGTTGGTGACACGTGCACAAAGATAGGGCGCTGGTAAAGCCACAAATGCTACAGCAG 1 PASS NS=1;SVTYPE=INS;SVLEN=212;READSOURCES=(0:5);UPSTREAM=AGTGTTT;DOWNSTREAM=.;CONTIG=AGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAGAATCACCACACTATACTGAATAGCTTGGTAAAAACCACAGCGCTTATGAGGGAAGTGCGGTTAGGAGCACAGCACTCCAAGACTTTGTTGGTGACACGTGCACAAAGATAGGGCGCTGGTAAAGCCACAAATGCTACAGCAG;CONTIG_NUM=3533;CLUSTER_NUM=4251;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991406 chr20:GROUPER:INS:0:2160 T TTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATG 2 PASS NS=1;SVTYPE=INS;SVLEN=60;READSOURCES=(0:3);UPSTREAM=AGTACCTT;DOWNSTREAM=.;CONTIG=AGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGT;CONTIG_NUM=3351;CLUSTER_NUM=4092;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991485 chr20:GROUPER:INS:0:2236;chr20:GROUPER:INS:0:2344;chr20:GROUPER:INS:0:2085;chr20:GROUPER:INS:0:2229 g gGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATC,gGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAA,gGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACAT,gGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGA 71 PASS NS=1;SVTYPE=INS;SVLEN=298;READSOURCES=(0:39);UPSTREAM=TCAGTGTAAGGAATAAACAAATACTTAAATTTGGGATCCTCACACCACAACTTCATAAGGGGGAGAGGG;DOWNSTREAM=.;CONTIG=TCAGTGTAAGGAATAAACAAATACTTAAATTTGGGATCCTCACACCACAACTTCATAAGGGGGAGAGGGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCG;CONTIG_NUM=3461;CLUSTER_NUM=4148;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 3/. ./. 4/. ./. ./. -chr20 56991486 chr20:GROUPER:INS:0:2509;chr20:GROUPER:INS:0:1995;chr20:GROUPER:INS:0:2380;chr20:GROUPER:INS:0:2145;chr20:GROUPER:INS:0:2146;chr20:GROUPER:INS:0:2218;chr20:GROUPER:INS:0:2229;chr20:GROUPER:INS:0:2032;chr20:GROUPER:INS:0:2159;chr20:GROUPER:INS:0:2271;chr20:GROUPER:INS:0:1864;chr20:GROUPER:INS:0:2224;chr20:GROUPER:INS:0:2273;chr20:GROUPER:INS:0:1958;chr20:GROUPER:INS:0:2079 G GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTAC,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGAGCTTGCATAGCTAT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGAGCTTGCATAGCTATTCTTTTTCCCCCCACTCTGAGTGC,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGAGCTTGCATAGCTATTCTTTTTCCCCCCACTCTGAGTGCTGAAGTGAT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCAT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAAC,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTA,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGAGCTTGCATAGCTATTCTTTTT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTC,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACT 88 PASS NS=1;SVTYPE=INS;SVLEN=429;READSOURCES=(0:42);UPSTREAM=TGAAGAAGAGGTCAGTGTAAGGAATAAACAAATACTTAAATTTGGGATCCTCACACCACAACTTCATAAGGGGGAGAGGG;DOWNSTREAM=.;CONTIG=TGAAGAAGAGGTCAGTGTAAGGAATAAACAAATACTTAAATTTGGGATCCTCACACCACAACTTCATAAGGGGGAGAGGGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGT;CONTIG_NUM=3856;CLUSTER_NUM=4429;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. 2/. ./. 3/. ./. ./. ./. 4/. 5/. ./. ./. ./. ./. ./. ./. ./. 6/. ./. 7/. ./. ./. 8/. ./. ./. ./. ./. ./. ./. 9/. ./. ./. ./. ./. ./. ./. ./. 10/. ./. 11/. ./. ./. 12/. ./. ./. 13/. ./. 14/. ./. ./. ./. ./. 15/. ./. -chr20 56991687 chr20:GROUPER:INS:0:2345 T TATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCA 1 PASS NS=1;SVTYPE=INS;SVLEN=104;READSOURCES=(0:2);UPSTREAM=TCAAATT;DOWNSTREAM=.;CONTIG=TCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCA;CONTIG_NUM=3593;CLUSTER_NUM=4335;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991955 chr20:GROUPER:INS:0:2078 g gCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGC 1 PASS NS=1;SVTYPE=INS;SVLEN=339;READSOURCES=(0:28);UPSTREAM=TGCCAGC;DOWNSTREAM=.;CONTIG=TGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCC;CONTIG_NUM=3168;CLUSTER_NUM=4008;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. -chr20 57002148 chr20:GROUPER:DEL:0:2136;chr20:GROUPER:DEL:0:2384;chr20:GROUPER:DEL:0:2228 ATGATGCAGGCGAAAGTGATCTGTGATCTGTTACCATTATGATGCAGGTCCATGATCTGTTACCATTATGATGCAGACGAAAGTGATCTGTGATCTGTTACCATTATGATGCAGGCGAAAGTGATCCGTGATCTGTTACAATTAT AGATGCAGGCGAAAGTGATCCGTGATCTGTTACAATTAT,A 78 PASS NS=1;SVTYPE=DEL;SVLEN=-106;READSOURCES=(0:2);UPSTREAM=CCATTATGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTA;DOWNSTREAM=GATGCAGGTGAAAGTGATCCGTG;CONTIG=CCATTATGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTAGATGCAGGTGAAAGTGATCCGTG;CONTIG_NUM=2933;CLUSTER_NUM=2903;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 57002329 chr20:GROUPER:DEL:0:2003;chr20:GROUPER:DEL:0:2035;chr20:GROUPER:DEL:0:2229;chr20:GROUPER:DEL:0:2088 ATGATGCAGGCGAAAGTGATCTGTGATCTGTGATCTGTTACCATTATGATGCAGGCGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGGTGAAGGTGGTCCGTGATCTGTTACCATTATGATGCAGGTCCATGATCTGTTACCATTATGATGCAGACGAAAGTGATTCGTGATCTGTTACCATTAT A 136 PASS NS=1;SVTYPE=DEL;SVLEN=-189;READSOURCES=(0:5);UPSTREAM=GTTACCATTATGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTAAGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTA;DOWNSTREAM=GATGCAGGTGAAAGTGATCC;CONTIG=GTTACCATTATGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTAAGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTAGATGCAGGTGAAAGTGATCC;CONTIG_NUM=2717;CLUSTER_NUM=2679;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. -chr20 57002412 chr20:GROUPER:DEL:0:2138;chr20:GROUPER:DEL:0:2104;chr20:GROUPER:DEL:0:2278 ATGATGCAGGTGAAGGTGGTCCGTGATCTGTTACCATTATGATGCAGGTCCATGATCTGTTACCATTATGATGCAGACGAAAGTGATTCGTGATCTGTTACCATTAT A 131 PASS NS=1;SVTYPE=DEL;SVLEN=-106;READSOURCES=(0:16);UPSTREAM=TGATCCGTGATCTGTTACCATTATGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTA;DOWNSTREAM=GATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGGCAAAAGTGATTTGTGATCTCGTAGCATTATGATGCAGGCAAA;CONTIG=TGATCCGTGATCTGTTACCATTATGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTAGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGGCAAAAGTGATTTGTGATCTCGTAGCATTATGATGCAGGCAAA;CONTIG_NUM=2935;CLUSTER_NUM=2905;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56990993 chr20:GROUPER:INS:0:2164 A ATGGAGAAATTCTCATGGAGTATTTCATCTGTGAAGGCGTCACTGCTCGTGGAATGAGAATAGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAG 1 PASS NS=1;SVTYPE=INS;SVLEN=113;READSOURCES=(0:4);UPSTREAM=AGCAAAT;DOWNSTREAM=.;CONTIG=AGCAAATGGAGAAATTCTCATGGAGTATTTCATCTGTGAAGGCGTCACTGCTCGTGGAATGAGAATAGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGT;CONTIG_NUM=3355;CLUSTER_NUM=4093;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991105 chr20:GROUPER:INS:0:2272 T TGGGGAACTGACTTAGAGTGTAGTGATAGGGTTGTTTGTGATAGGCAGGTAAGCAAATGGAGAAATTCTCATGGAGTATTTCATCTGTGAAGGCGTCACTGCTCGTGGAATGAGAATAGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAG 2 PASS NS=1;SVTYPE=INS;SVLEN=193;READSOURCES=(0:8);UPSTREAM=TTTTCAGT;DOWNSTREAM=.;CONTIG=TTTTCAGTGGGGAACTGACTTAGAGTGTAGTGATAGGGTTGTTTGTGATAGGCAGGTAAGCAAATGGAGAAATTCTCATGGAGTATTTCATCTGTGAAGGCGTCACTGCTCGTGGAATGAGAATAGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAG;CONTIG_NUM=3531;CLUSTER_NUM=4250;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991110 chr20:GROUPER:INS:0:2162 T TCAGTTCTGCTGTAATGCATTCCTGGAGAATCACCACACTATACTGAATAGCTTGGTAAAAACCACAGCGCTTATGAGGGAAGTGCGGTTAGGAGCACAGCACTCCAAGACTTTGTTGGTGACACGTGCACAAAGATAGGGCGCTGG 2 PASS NS=1;SVTYPE=INS;SVLEN=146;READSOURCES=(0:13);UPSTREAM=AGTATAGT;DOWNSTREAM=.;CONTIG=AGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAGAATCACCACACTATACTGAATAGCTTGGTAAAAACCACAGCGCTTATGAGGGAAGTGCGGTTAGGAGCACAGCACTCCAAGACTTTGTTGGTGACACGTGCACAAAGATAGGGCGCTGG;CONTIG_NUM=3353;CLUSTER_NUM=4093;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991372 chr20:GROUPER:INS:0:2274 T TGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAGAATCACCACACTATACTGAATAGCTTGGTAAAAACCACAGCGCTTATGAGGGAAGTGCGGTTAGGAGCACAGCACTCCAAGACTTTGTTGGTGACACGTGCACAAAGATAGGGCGCTGGTAAAGCCACAAATGCTACAGCAG 1 PASS NS=1;SVTYPE=INS;SVLEN=212;READSOURCES=(0:5);UPSTREAM=AGTGTTT;DOWNSTREAM=.;CONTIG=AGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAGAATCACCACACTATACTGAATAGCTTGGTAAAAACCACAGCGCTTATGAGGGAAGTGCGGTTAGGAGCACAGCACTCCAAGACTTTGTTGGTGACACGTGCACAAAGATAGGGCGCTGGTAAAGCCACAAATGCTACAGCAG;CONTIG_NUM=3533;CLUSTER_NUM=4251;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991406 chr20:GROUPER:INS:0:2160 T TTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATG 2 PASS NS=1;SVTYPE=INS;SVLEN=60;READSOURCES=(0:3);UPSTREAM=AGTACCTT;DOWNSTREAM=.;CONTIG=AGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGT;CONTIG_NUM=3351;CLUSTER_NUM=4092;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991485 chr20:GROUPER:INS:0:2236;chr20:GROUPER:INS:0:2344;chr20:GROUPER:INS:0:2085;chr20:GROUPER:INS:0:2229 g gGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATC,gGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAA,gGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACAT,gGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGA 71 PASS NS=1;SVTYPE=INS;SVLEN=298;READSOURCES=(0:39);UPSTREAM=TCAGTGTAAGGAATAAACAAATACTTAAATTTGGGATCCTCACACCACAACTTCATAAGGGGGAGAGGG;DOWNSTREAM=.;CONTIG=TCAGTGTAAGGAATAAACAAATACTTAAATTTGGGATCCTCACACCACAACTTCATAAGGGGGAGAGGGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCG;CONTIG_NUM=3461;CLUSTER_NUM=4148;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 3/. ./. 4/. ./. ./. -chr20 56991486 chr20:GROUPER:INS:0:2509;chr20:GROUPER:INS:0:1995;chr20:GROUPER:INS:0:2380;chr20:GROUPER:INS:0:2145;chr20:GROUPER:INS:0:2146;chr20:GROUPER:INS:0:2218;chr20:GROUPER:INS:0:2229;chr20:GROUPER:INS:0:2032;chr20:GROUPER:INS:0:2159;chr20:GROUPER:INS:0:2271;chr20:GROUPER:INS:0:1864;chr20:GROUPER:INS:0:2224;chr20:GROUPER:INS:0:2273;chr20:GROUPER:INS:0:1958;chr20:GROUPER:INS:0:2079 G GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTAC,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGAGCTTGCATAGCTAT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGAGCTTGCATAGCTATTCTTTTTCCCCCCACTCTGAGTGC,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGAGCTTGCATAGCTATTCTTTTTCCCCCCACTCTGAGTGCTGAAGTGAT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCAT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAAC,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTA,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGAGCTTGCATAGCTATTCTTTTT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTC,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACT 88 PASS NS=1;SVTYPE=INS;SVLEN=429;READSOURCES=(0:42);UPSTREAM=TGAAGAAGAGGTCAGTGTAAGGAATAAACAAATACTTAAATTTGGGATCCTCACACCACAACTTCATAAGGGGGAGAGGG;DOWNSTREAM=.;CONTIG=TGAAGAAGAGGTCAGTGTAAGGAATAAACAAATACTTAAATTTGGGATCCTCACACCACAACTTCATAAGGGGGAGAGGGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGT;CONTIG_NUM=3856;CLUSTER_NUM=4429;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. 2/. ./. 3/. ./. ./. ./. 4/. 5/. ./. ./. ./. ./. ./. ./. ./. 6/. ./. 7/. ./. ./. 8/. ./. ./. ./. ./. ./. ./. 9/. ./. ./. ./. ./. ./. ./. ./. 10/. ./. 11/. ./. ./. 12/. ./. ./. 13/. ./. 14/. ./. ./. ./. ./. 15/. ./. -chr20 56991687 chr20:GROUPER:INS:0:2345 T TATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCA 1 PASS NS=1;SVTYPE=INS;SVLEN=104;READSOURCES=(0:2);UPSTREAM=TCAAATT;DOWNSTREAM=.;CONTIG=TCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCA;CONTIG_NUM=3593;CLUSTER_NUM=4335;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991955 chr20:GROUPER:INS:0:2078 g gCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGC 1 PASS NS=1;SVTYPE=INS;SVLEN=339;READSOURCES=(0:28);UPSTREAM=TGCCAGC;DOWNSTREAM=.;CONTIG=TGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCC;CONTIG_NUM=3168;CLUSTER_NUM=4008;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. -chr20 57002148 chr20:GROUPER:DEL:0:2136;chr20:GROUPER:DEL:0:2384;chr20:GROUPER:DEL:0:2228 ATGATGCAGGCGAAAGTGATCTGTGATCTGTTACCATTATGATGCAGGTCCATGATCTGTTACCATTATGATGCAGACGAAAGTGATCTGTGATCTGTTACCATTATGATGCAGGCGAAAGTGATCCGTGATCTGTTACAATTAT AGATGCAGGCGAAAGTGATCCGTGATCTGTTACAATTAT,A 78 PASS NS=1;SVTYPE=DEL;SVLEN=-106;READSOURCES=(0:2);UPSTREAM=CCATTATGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTA;DOWNSTREAM=GATGCAGGTGAAAGTGATCCGTG;CONTIG=CCATTATGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTAGATGCAGGTGAAAGTGATCCGTG;CONTIG_NUM=2933;CLUSTER_NUM=2903;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 57002329 chr20:GROUPER:DEL:0:2003;chr20:GROUPER:DEL:0:2035;chr20:GROUPER:DEL:0:2229;chr20:GROUPER:DEL:0:2088 ATGATGCAGGCGAAAGTGATCTGTGATCTGTGATCTGTTACCATTATGATGCAGGCGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGGTGAAGGTGGTCCGTGATCTGTTACCATTATGATGCAGGTCCATGATCTGTTACCATTATGATGCAGACGAAAGTGATTCGTGATCTGTTACCATTAT A 136 PASS NS=1;SVTYPE=DEL;SVLEN=-189;READSOURCES=(0:5);UPSTREAM=GTTACCATTATGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTAAGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTA;DOWNSTREAM=GATGCAGGTGAAAGTGATCC;CONTIG=GTTACCATTATGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTAAGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTAGATGCAGGTGAAAGTGATCC;CONTIG_NUM=2717;CLUSTER_NUM=2679;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. -chr20 57002412 chr20:GROUPER:DEL:0:2138;chr20:GROUPER:DEL:0:2104;chr20:GROUPER:DEL:0:2278 ATGATGCAGGTGAAGGTGGTCCGTGATCTGTTACCATTATGATGCAGGTCCATGATCTGTTACCATTATGATGCAGACGAAAGTGATTCGTGATCTGTTACCATTAT A 131 PASS NS=1;SVTYPE=DEL;SVLEN=-106;READSOURCES=(0:16);UPSTREAM=TGATCCGTGATCTGTTACCATTATGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTA;DOWNSTREAM=GATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGGCAAAAGTGATTTGTGATCTCGTAGCATTATGATGCAGGCAAA;CONTIG=TGATCCGTGATCTGTTACCATTATGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTAGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGGCAAAAGTGATTTGTGATCTCGTAGCATTATGATGCAGGCAAA;CONTIG_NUM=2935;CLUSTER_NUM=2905;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56990993 chr20:GROUPER:INS:0:2164 A ATGGAGAAATTCTCATGGAGTATTTCATCTGTGAAGGCGTCACTGCTCGTGGAATGAGAATAGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAG 1 PASS NS=1;SVTYPE=INS;SVLEN=113;READSOURCES=(0:4);UPSTREAM=AGCAAAT;DOWNSTREAM=.;CONTIG=AGCAAATGGAGAAATTCTCATGGAGTATTTCATCTGTGAAGGCGTCACTGCTCGTGGAATGAGAATAGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGT;CONTIG_NUM=3355;CLUSTER_NUM=4093;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991105 chr20:GROUPER:INS:0:2272 T TGGGGAACTGACTTAGAGTGTAGTGATAGGGTTGTTTGTGATAGGCAGGTAAGCAAATGGAGAAATTCTCATGGAGTATTTCATCTGTGAAGGCGTCACTGCTCGTGGAATGAGAATAGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAG 2 PASS NS=1;SVTYPE=INS;SVLEN=193;READSOURCES=(0:8);UPSTREAM=TTTTCAGT;DOWNSTREAM=.;CONTIG=TTTTCAGTGGGGAACTGACTTAGAGTGTAGTGATAGGGTTGTTTGTGATAGGCAGGTAAGCAAATGGAGAAATTCTCATGGAGTATTTCATCTGTGAAGGCGTCACTGCTCGTGGAATGAGAATAGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAG;CONTIG_NUM=3531;CLUSTER_NUM=4250;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991110 chr20:GROUPER:INS:0:2162 T TCAGTTCTGCTGTAATGCATTCCTGGAGAATCACCACACTATACTGAATAGCTTGGTAAAAACCACAGCGCTTATGAGGGAAGTGCGGTTAGGAGCACAGCACTCCAAGACTTTGTTGGTGACACGTGCACAAAGATAGGGCGCTGG 2 PASS NS=1;SVTYPE=INS;SVLEN=146;READSOURCES=(0:13);UPSTREAM=AGTATAGT;DOWNSTREAM=.;CONTIG=AGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAGAATCACCACACTATACTGAATAGCTTGGTAAAAACCACAGCGCTTATGAGGGAAGTGCGGTTAGGAGCACAGCACTCCAAGACTTTGTTGGTGACACGTGCACAAAGATAGGGCGCTGG;CONTIG_NUM=3353;CLUSTER_NUM=4093;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991372 chr20:GROUPER:INS:0:2274 T TGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAGAATCACCACACTATACTGAATAGCTTGGTAAAAACCACAGCGCTTATGAGGGAAGTGCGGTTAGGAGCACAGCACTCCAAGACTTTGTTGGTGACACGTGCACAAAGATAGGGCGCTGGTAAAGCCACAAATGCTACAGCAG 1 PASS NS=1;SVTYPE=INS;SVLEN=212;READSOURCES=(0:5);UPSTREAM=AGTGTTT;DOWNSTREAM=.;CONTIG=AGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAGAATCACCACACTATACTGAATAGCTTGGTAAAAACCACAGCGCTTATGAGGGAAGTGCGGTTAGGAGCACAGCACTCCAAGACTTTGTTGGTGACACGTGCACAAAGATAGGGCGCTGGTAAAGCCACAAATGCTACAGCAG;CONTIG_NUM=3533;CLUSTER_NUM=4251;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991406 chr20:GROUPER:INS:0:2160 T TTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATG 2 PASS NS=1;SVTYPE=INS;SVLEN=60;READSOURCES=(0:3);UPSTREAM=AGTACCTT;DOWNSTREAM=.;CONTIG=AGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGT;CONTIG_NUM=3351;CLUSTER_NUM=4092;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991485 chr20:GROUPER:INS:0:2236;chr20:GROUPER:INS:0:2344;chr20:GROUPER:INS:0:2085;chr20:GROUPER:INS:0:2229 g gGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATC,gGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAA,gGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACAT,gGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGA 71 PASS NS=1;SVTYPE=INS;SVLEN=298;READSOURCES=(0:39);UPSTREAM=TCAGTGTAAGGAATAAACAAATACTTAAATTTGGGATCCTCACACCACAACTTCATAAGGGGGAGAGGG;DOWNSTREAM=.;CONTIG=TCAGTGTAAGGAATAAACAAATACTTAAATTTGGGATCCTCACACCACAACTTCATAAGGGGGAGAGGGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCG;CONTIG_NUM=3461;CLUSTER_NUM=4148;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 3/. ./. 4/. ./. ./. -chr20 56991486 chr20:GROUPER:INS:0:2509;chr20:GROUPER:INS:0:1995;chr20:GROUPER:INS:0:2380;chr20:GROUPER:INS:0:2145;chr20:GROUPER:INS:0:2146;chr20:GROUPER:INS:0:2218;chr20:GROUPER:INS:0:2229;chr20:GROUPER:INS:0:2032;chr20:GROUPER:INS:0:2159;chr20:GROUPER:INS:0:2271;chr20:GROUPER:INS:0:1864;chr20:GROUPER:INS:0:2224;chr20:GROUPER:INS:0:2273;chr20:GROUPER:INS:0:1958;chr20:GROUPER:INS:0:2079 G GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTAC,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGAGCTTGCATAGCTAT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGAGCTTGCATAGCTATTCTTTTTCCCCCCACTCTGAGTGC,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGAGCTTGCATAGCTATTCTTTTTCCCCCCACTCTGAGTGCTGAAGTGAT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCAT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAAC,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTA,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGAGCTTGCATAGCTATTCTTTTT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTC,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACT 88 PASS NS=1;SVTYPE=INS;SVLEN=429;READSOURCES=(0:42);UPSTREAM=TGAAGAAGAGGTCAGTGTAAGGAATAAACAAATACTTAAATTTGGGATCCTCACACCACAACTTCATAAGGGGGAGAGGG;DOWNSTREAM=.;CONTIG=TGAAGAAGAGGTCAGTGTAAGGAATAAACAAATACTTAAATTTGGGATCCTCACACCACAACTTCATAAGGGGGAGAGGGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGT;CONTIG_NUM=3856;CLUSTER_NUM=4429;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. 2/. ./. 3/. ./. ./. ./. 4/. 5/. ./. ./. ./. ./. ./. ./. ./. 6/. ./. 7/. ./. ./. 8/. ./. ./. ./. ./. ./. ./. 9/. ./. ./. ./. ./. ./. ./. ./. 10/. ./. 11/. ./. ./. 12/. ./. ./. 13/. ./. 14/. ./. ./. ./. ./. 15/. ./. -chr20 56991687 chr20:GROUPER:INS:0:2345 T TATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCA 1 PASS NS=1;SVTYPE=INS;SVLEN=104;READSOURCES=(0:2);UPSTREAM=TCAAATT;DOWNSTREAM=.;CONTIG=TCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCA;CONTIG_NUM=3593;CLUSTER_NUM=4335;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991955 chr20:GROUPER:INS:0:2078 g gCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGC 1 PASS NS=1;SVTYPE=INS;SVLEN=339;READSOURCES=(0:28);UPSTREAM=TGCCAGC;DOWNSTREAM=.;CONTIG=TGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCC;CONTIG_NUM=3168;CLUSTER_NUM=4008;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. -chr20 57002148 chr20:GROUPER:DEL:0:2136;chr20:GROUPER:DEL:0:2384;chr20:GROUPER:DEL:0:2228 ATGATGCAGGCGAAAGTGATCTGTGATCTGTTACCATTATGATGCAGGTCCATGATCTGTTACCATTATGATGCAGACGAAAGTGATCTGTGATCTGTTACCATTATGATGCAGGCGAAAGTGATCCGTGATCTGTTACAATTAT AGATGCAGGCGAAAGTGATCCGTGATCTGTTACAATTAT,A 78 PASS NS=1;SVTYPE=DEL;SVLEN=-106;READSOURCES=(0:2);UPSTREAM=CCATTATGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTA;DOWNSTREAM=GATGCAGGTGAAAGTGATCCGTG;CONTIG=CCATTATGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTAGATGCAGGTGAAAGTGATCCGTG;CONTIG_NUM=2933;CLUSTER_NUM=2903;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 57002329 chr20:GROUPER:DEL:0:2003;chr20:GROUPER:DEL:0:2035;chr20:GROUPER:DEL:0:2229;chr20:GROUPER:DEL:0:2088 ATGATGCAGGCGAAAGTGATCTGTGATCTGTGATCTGTTACCATTATGATGCAGGCGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGGTGAAGGTGGTCCGTGATCTGTTACCATTATGATGCAGGTCCATGATCTGTTACCATTATGATGCAGACGAAAGTGATTCGTGATCTGTTACCATTAT A 136 PASS NS=1;SVTYPE=DEL;SVLEN=-189;READSOURCES=(0:5);UPSTREAM=GTTACCATTATGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTAAGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTA;DOWNSTREAM=GATGCAGGTGAAAGTGATCC;CONTIG=GTTACCATTATGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTAAGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTAGATGCAGGTGAAAGTGATCC;CONTIG_NUM=2717;CLUSTER_NUM=2679;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. -chr20 57002412 chr20:GROUPER:DEL:0:2138;chr20:GROUPER:DEL:0:2104;chr20:GROUPER:DEL:0:2278 ATGATGCAGGTGAAGGTGGTCCGTGATCTGTTACCATTATGATGCAGGTCCATGATCTGTTACCATTATGATGCAGACGAAAGTGATTCGTGATCTGTTACCATTAT A 131 PASS NS=1;SVTYPE=DEL;SVLEN=-106;READSOURCES=(0:16);UPSTREAM=TGATCCGTGATCTGTTACCATTATGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTA;DOWNSTREAM=GATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGGCAAAAGTGATTTGTGATCTCGTAGCATTATGATGCAGGCAAA;CONTIG=TGATCCGTGATCTGTTACCATTATGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTAGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGGCAAAAGTGATTTGTGATCTCGTAGCATTATGATGCAGGCAAA;CONTIG_NUM=2935;CLUSTER_NUM=2905;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56990993 chr20:GROUPER:INS:0:2164 A ATGGAGAAATTCTCATGGAGTATTTCATCTGTGAAGGCGTCACTGCTCGTGGAATGAGAATAGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAG 1 PASS NS=1;SVTYPE=INS;SVLEN=113;READSOURCES=(0:4);UPSTREAM=AGCAAAT;DOWNSTREAM=.;CONTIG=AGCAAATGGAGAAATTCTCATGGAGTATTTCATCTGTGAAGGCGTCACTGCTCGTGGAATGAGAATAGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGT;CONTIG_NUM=3355;CLUSTER_NUM=4093;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991105 chr20:GROUPER:INS:0:2272 T TGGGGAACTGACTTAGAGTGTAGTGATAGGGTTGTTTGTGATAGGCAGGTAAGCAAATGGAGAAATTCTCATGGAGTATTTCATCTGTGAAGGCGTCACTGCTCGTGGAATGAGAATAGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAG 2 PASS NS=1;SVTYPE=INS;SVLEN=193;READSOURCES=(0:8);UPSTREAM=TTTTCAGT;DOWNSTREAM=.;CONTIG=TTTTCAGTGGGGAACTGACTTAGAGTGTAGTGATAGGGTTGTTTGTGATAGGCAGGTAAGCAAATGGAGAAATTCTCATGGAGTATTTCATCTGTGAAGGCGTCACTGCTCGTGGAATGAGAATAGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAG;CONTIG_NUM=3531;CLUSTER_NUM=4250;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991110 chr20:GROUPER:INS:0:2162 T TCAGTTCTGCTGTAATGCATTCCTGGAGAATCACCACACTATACTGAATAGCTTGGTAAAAACCACAGCGCTTATGAGGGAAGTGCGGTTAGGAGCACAGCACTCCAAGACTTTGTTGGTGACACGTGCACAAAGATAGGGCGCTGG 2 PASS NS=1;SVTYPE=INS;SVLEN=146;READSOURCES=(0:13);UPSTREAM=AGTATAGT;DOWNSTREAM=.;CONTIG=AGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAGAATCACCACACTATACTGAATAGCTTGGTAAAAACCACAGCGCTTATGAGGGAAGTGCGGTTAGGAGCACAGCACTCCAAGACTTTGTTGGTGACACGTGCACAAAGATAGGGCGCTGG;CONTIG_NUM=3353;CLUSTER_NUM=4093;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991372 chr20:GROUPER:INS:0:2274 T TGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAGAATCACCACACTATACTGAATAGCTTGGTAAAAACCACAGCGCTTATGAGGGAAGTGCGGTTAGGAGCACAGCACTCCAAGACTTTGTTGGTGACACGTGCACAAAGATAGGGCGCTGGTAAAGCCACAAATGCTACAGCAG 1 PASS NS=1;SVTYPE=INS;SVLEN=212;READSOURCES=(0:5);UPSTREAM=AGTGTTT;DOWNSTREAM=.;CONTIG=AGTGTTTGCAATAATAATTCACAGAACAATAAATGATGCAGTAGTATAGTCAGTTCTGCTGTAATGCATTCCTGGAGAATCACCACACTATACTGAATAGCTTGGTAAAAACCACAGCGCTTATGAGGGAAGTGCGGTTAGGAGCACAGCACTCCAAGACTTTGTTGGTGACACGTGCACAAAGATAGGGCGCTGGTAAAGCCACAAATGCTACAGCAG;CONTIG_NUM=3533;CLUSTER_NUM=4251;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991406 chr20:GROUPER:INS:0:2160 T TTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATG 2 PASS NS=1;SVTYPE=INS;SVLEN=60;READSOURCES=(0:3);UPSTREAM=AGTACCTT;DOWNSTREAM=.;CONTIG=AGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGT;CONTIG_NUM=3351;CLUSTER_NUM=4092;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991485 chr20:GROUPER:INS:0:2236;chr20:GROUPER:INS:0:2344;chr20:GROUPER:INS:0:2085;chr20:GROUPER:INS:0:2229 g gGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATC,gGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAA,gGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACAT,gGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGA 71 PASS NS=1;SVTYPE=INS;SVLEN=298;READSOURCES=(0:39);UPSTREAM=TCAGTGTAAGGAATAAACAAATACTTAAATTTGGGATCCTCACACCACAACTTCATAAGGGGGAGAGGG;DOWNSTREAM=.;CONTIG=TCAGTGTAAGGAATAAACAAATACTTAAATTTGGGATCCTCACACCACAACTTCATAAGGGGGAGAGGGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCG;CONTIG_NUM=3461;CLUSTER_NUM=4148;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 3/. ./. 4/. ./. ./. -chr20 56991486 chr20:GROUPER:INS:0:2509;chr20:GROUPER:INS:0:1995;chr20:GROUPER:INS:0:2380;chr20:GROUPER:INS:0:2145;chr20:GROUPER:INS:0:2146;chr20:GROUPER:INS:0:2218;chr20:GROUPER:INS:0:2229;chr20:GROUPER:INS:0:2032;chr20:GROUPER:INS:0:2159;chr20:GROUPER:INS:0:2271;chr20:GROUPER:INS:0:1864;chr20:GROUPER:INS:0:2224;chr20:GROUPER:INS:0:2273;chr20:GROUPER:INS:0:1958;chr20:GROUPER:INS:0:2079 G GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTAC,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGAGCTTGCATAGCTAT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGAGCTTGCATAGCTATTCTTTTTCCCCCCACTCTGAGTGC,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGAGCTTGCATAGCTATTCTTTTTCCCCCCACTCTGAGTGCTGAAGTGAT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCAT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAAC,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTA,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGTTCTTCTGAGTTGCAGTTTTTAGATGAGGGTCAGGGAATGCATGTACATGGTGATTTGCTTGTGACCTCTTTAGGTTTGTGTGCCCTTTATGCCTGTCTGTGTGTGTGTTTTATTGCTGGTTTGACCCTAGAAAATCAGAGCTTGCATAGCTATTCTTTTT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTC,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTT,GAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACT 88 PASS NS=1;SVTYPE=INS;SVLEN=429;READSOURCES=(0:42);UPSTREAM=TGAAGAAGAGGTCAGTGTAAGGAATAAACAAATACTTAAATTTGGGATCCTCACACCACAACTTCATAAGGGGGAGAGGG;DOWNSTREAM=.;CONTIG=TGAAGAAGAGGTCAGTGTAAGGAATAAACAAATACTTAAATTTGGGATCCTCACACCACAACTTCATAAGGGGGAGAGGGAAGGAAGAAACTAGTAACTGAATTGGAAACTAGCAAATATTCTGGATTTCATCACAGTGGAATCTTGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCCGCTGTGCTTATGTGGAGT;CONTIG_NUM=3856;CLUSTER_NUM=4429;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. 2/. ./. 3/. ./. ./. ./. 4/. 5/. ./. ./. ./. ./. ./. ./. ./. 6/. ./. 7/. ./. ./. 8/. ./. ./. ./. ./. ./. ./. 9/. ./. ./. ./. ./. ./. ./. ./. 10/. ./. 11/. ./. ./. 12/. ./. ./. 13/. ./. 14/. ./. ./. ./. ./. 15/. ./. -chr20 56991687 chr20:GROUPER:INS:0:2345 T TATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCA 1 PASS NS=1;SVTYPE=INS;SVLEN=104;READSOURCES=(0:2);UPSTREAM=TCAAATT;DOWNSTREAM=.;CONTIG=TCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCA;CONTIG_NUM=3593;CLUSTER_NUM=4335;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 56991955 chr20:GROUPER:INS:0:2078 g gCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGC 1 PASS NS=1;SVTYPE=INS;SVLEN=339;READSOURCES=(0:28);UPSTREAM=TGCCAGC;DOWNSTREAM=.;CONTIG=TGCCAGCATCTCGGTTTTCTGCTCTCACTATACTTCAAACCATTTTAGAAAAAAAGATCTATGTATTTTTGGGTGTTTTGGGGACCATTATGAATTCTTGGCGTTCTGCTCTGAAGATACTTCCGTGTTTCTGAGGCAGAATCTTGTTGAAACTAGTAACTTTAAGCTTTGATTAAGCTTTGATTTAGAACGCTTTGTGGCCTGAGAGTTTCTGAATGACATTCAAATTATCGTTGAGTACCTTTCATCCCTAGGCTTTATATTTGAAAACTCACCCCATTTCCGGTGTCTCTTTATGTCATGTACATTTTTGTCCTCTTTTTTCTCCCCCCAGTGTTGTGGTGCC;CONTIG_NUM=3168;CLUSTER_NUM=4008;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. -chr20 57002148 chr20:GROUPER:DEL:0:2136;chr20:GROUPER:DEL:0:2384;chr20:GROUPER:DEL:0:2228 ATGATGCAGGCGAAAGTGATCTGTGATCTGTTACCATTATGATGCAGGTCCATGATCTGTTACCATTATGATGCAGACGAAAGTGATCTGTGATCTGTTACCATTATGATGCAGGCGAAAGTGATCCGTGATCTGTTACAATTAT AGATGCAGGCGAAAGTGATCCGTGATCTGTTACAATTAT,A 78 PASS NS=1;SVTYPE=DEL;SVLEN=-106;READSOURCES=(0:2);UPSTREAM=CCATTATGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTA;DOWNSTREAM=GATGCAGGTGAAAGTGATCCGTG;CONTIG=CCATTATGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTAGATGCAGGTGAAAGTGATCCGTG;CONTIG_NUM=2933;CLUSTER_NUM=2903;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 2/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr20 57002329 chr20:GROUPER:DEL:0:2003;chr20:GROUPER:DEL:0:2035;chr20:GROUPER:DEL:0:2229;chr20:GROUPER:DEL:0:2088 ATGATGCAGGCGAAAGTGATCTGTGATCTGTGATCTGTTACCATTATGATGCAGGCGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGGTGAAGGTGGTCCGTGATCTGTTACCATTATGATGCAGGTCCATGATCTGTTACCATTATGATGCAGACGAAAGTGATTCGTGATCTGTTACCATTAT A 136 PASS NS=1;SVTYPE=DEL;SVLEN=-189;READSOURCES=(0:5);UPSTREAM=GTTACCATTATGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTAAGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTA;DOWNSTREAM=GATGCAGGTGAAAGTGATCC;CONTIG=GTTACCATTATGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTAAGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTAGATGCAGGTGAAAGTGATCC;CONTIG_NUM=2717;CLUSTER_NUM=2679;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. -chr20 57002412 chr20:GROUPER:DEL:0:2138;chr20:GROUPER:DEL:0:2104;chr20:GROUPER:DEL:0:2278 ATGATGCAGGTGAAGGTGGTCCGTGATCTGTTACCATTATGATGCAGGTCCATGATCTGTTACCATTATGATGCAGACGAAAGTGATTCGTGATCTGTTACCATTAT A 131 PASS NS=1;SVTYPE=DEL;SVLEN=-106;READSOURCES=(0:16);UPSTREAM=TGATCCGTGATCTGTTACCATTATGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTA;DOWNSTREAM=GATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGGCAAAAGTGATTTGTGATCTCGTAGCATTATGATGCAGGCAAA;CONTIG=TGATCCGTGATCTGTTACCATTATGATGCAGACGAAAGTGATCCGTGATCTGTTACCATTAGATGCAGGTGAAAGTGATCCGTGATCTGTTACCATTATGATGCAGGCAAAAGTGATTTGTGATCTCGTAGCATTATGATGCAGGCAAA;CONTIG_NUM=2935;CLUSTER_NUM=2905;ensembl_gene_id=ENSG00000124164 GT ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/. ./. ./. ./. ./. ./. ./. ./. ./. diff --git a/VariantSurvival_package/R/metadata.xlsx b/VariantSurvival_package/R/metadata.xlsx 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gene-annotated
callset
gene-annotate...
variant
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variant...
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variant...
variant
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variant...
seq-to-ref
alignment
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Merge + QC + Annotation
Merge + QC + Annotation
Variant Caller 1
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...
...
...
...Medical ConditionAlzheimer's diseaseALS...Gene listPLCG2TREM2...
Per individual
Per individual
[Optional]
Recommend caller according to known SV type affecting selected genes
[Optional]...
Survival Analysis
Survival Analysis
Genotype-treatment
response profile
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Patient ID
Patient ID
Var 1
Var 1
Var ...
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5
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1
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9
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0
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0
00134
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Patient ID
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gene-annotated
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gene-annotate...
Survival Analysis
Survival Analysis
Genotype-treatment
response profile
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VariantSurvival
(shiny dashboard)
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TreatmentMedical ConditionAlzheimer's diseaseALS...Text is not SVG - cannot display \ No newline at end of file diff --git a/img/barplot.png b/img/barplot.png deleted file mode 100644 index 1108809..0000000 Binary files a/img/barplot.png and /dev/null differ diff --git a/img/dashboard.png b/img/dashboard.png deleted file mode 100644 index 4d184d3..0000000 Binary files a/img/dashboard.png and /dev/null differ diff --git a/img/survivalplot2.png b/img/survivalplot2.png deleted file mode 100644 index 866d99a..0000000 Binary files a/img/survivalplot2.png and /dev/null differ diff --git a/img/table2.png b/img/table2.png deleted file mode 100644 index 095880f..0000000 Binary files a/img/table2.png and /dev/null differ diff --git a/VariantSurvival_package/DESCRIPTION b/variantsurvival/DESCRIPTION similarity index 58% rename from VariantSurvival_package/DESCRIPTION rename to variantsurvival/DESCRIPTION index 9f5b6f2..30f5f6c 100644 --- a/VariantSurvival_package/DESCRIPTION +++ b/variantsurvival/DESCRIPTION @@ -6,23 +6,28 @@ Author: person("Hiba", "Ben Aribi", , "benaribi.hiba@gmail.com", role = c("aut", comment = c(ORCID = "0000-0001-9547-8725")) Maintainer: The package maintainer Description: Survival analysis and data visualization. -License: GPL-3 +License: MIT Encoding: UTF-8 LazyData: true -RoxygenNote: 7.2.1 +RoxygenNote: 7.2.3 Imports: - dplyr, - DT, - ggplot2, - ggsurvfit, - gtsummary, - lubridate, - readr, - readxl, - shiny, - shinydashboard, - survival, - survminer, - vcfR + shiny, + shinyjs, + shinydashboard, + shinythemes, + shinyWidgets, + shinycssloaders, + DT, + dplyr, + vcfR, + readr, + readxl, + ggsurvfit, + survival, + ggplot2, + survminer, + lubridate, + gtsummary Depends: + R (>= 2.10), tidyverse diff --git a/VariantSurvival_package/NAMESPACE b/variantsurvival/NAMESPACE similarity index 95% rename from VariantSurvival_package/NAMESPACE rename to variantsurvival/NAMESPACE index 09ec63a..88892fe 100644 --- a/VariantSurvival_package/NAMESPACE +++ b/variantsurvival/NAMESPACE @@ -1,3 +1,3 @@ -# Generated by roxygen2: do not edit by hand - -export(VariantSurvival) +# Generated by roxygen2: do not edit by hand + +export(VariantSurvival) diff --git a/variantsurvival/R/CountSVsDf.R b/variantsurvival/R/CountSVsDf.R new file mode 100644 index 0000000..9573fee --- /dev/null +++ b/variantsurvival/R/CountSVsDf.R @@ -0,0 +1,37 @@ +#' `CountSVsDf` +#' @param ncol name column +#' @param nrow name row +#' @param disease_genes_names disease name +#' @param sample_names sample name +#' @param genes_with_svs_in_sample gene +#' @param vcf file +#' @return sample_disease_gene_df +#' @noRd +CountSVsDf <- function(ncol, nrow, + disease_genes_names, + sample_names, + genes_with_svs_in_sample, + vcf, + ids_col){ + sample_disease_gene_df <- data.frame(matrix(0, ncol = ncol, nrow = nrow)) + colnames(sample_disease_gene_df) <- disease_genes_names + rownames(sample_disease_gene_df) <- sample_names + + for (sv_idx in 1:length(genes_with_svs_in_sample)) { + # if the sv is in a gene of interest + sv_gene_name <- genes_with_svs_in_sample[sv_idx] + if(is.na(sv_gene_name)) + next + for(individual_idx in 1:length(sample_names)){ + indiv_id <- sample_names[individual_idx] + gt <- vcf@gt[sv_idx, indiv_id] + if(!is.na(gt)) + { + sample_disease_gene_df[indiv_id, sv_gene_name] %+=% 1 + } + } + } + sample_disease_gene_df <- (rownames_to_column(sample_disease_gene_df,ids_col) + %>% rename(ids = ids_col)) + return(sample_disease_gene_df) +} diff --git a/variantsurvival/R/RemoveNAs.R b/variantsurvival/R/RemoveNAs.R new file mode 100644 index 0000000..8a0832e --- /dev/null +++ b/variantsurvival/R/RemoveNAs.R @@ -0,0 +1,18 @@ +#' `RemoveNAs` removes all rows with Na +#' entries in the time factor column. +#' @param df: metadata data frame +#' @param time_col: time factor input +#' @return df +#' @noRd +RemoveNAs <- function(df, time_col) { + entries <- df[[time_col]] + nas_entries <- is.na(entries) + NAs_entries <- entries=="NA" + if (sum(nas_entries) > 0){ + return(df[!nas_entries,]) + } else if (sum(NAs_entries) > 0){ + return(df[!NAs_entries,]) + } else { + return(df) + } +} diff --git a/variantsurvival/R/VariantSurvival.R b/variantsurvival/R/VariantSurvival.R new file mode 100644 index 0000000..ed56947 --- /dev/null +++ b/variantsurvival/R/VariantSurvival.R @@ -0,0 +1,822 @@ +#' VariantSurvival +#' +#' @param vcffile path to the vcf file containing the Structural variant data +#' @param metadatafile path to the txt file containing the samples metadata +#' @param demo true or false +#' @export + +VariantSurvival <- function(vcffile, metadatafile,demo=FALSE){ + load() + ## read input + #demo or input files + if (demo==TRUE){ + vcf <- VariantSurvival:::vcf_demo + metadata <- VariantSurvival:::metadata_demo + } else if (demo==FALSE){ + vcf <- vcfR::read.vcfR(vcffile, verbose = FALSE) + metadata <- readxl::read_excel(metadatafile) + } + metadata <- na.omit(metadata) + #system data + disease_gene <-VariantSurvival:::disease_gene + disease_type_gene <- VariantSurvival:::disease_type_gene + gene_ids_table <- VariantSurvival:::gene_ids_table + rownames(gene_ids_table) <- gene_ids_table$ensembleID + days_year <- 365.25 + ## run app + ui <- bootstrapPage( + navbarPage(theme = shinytheme("flatly"), + collapsible = TRUE, + HTML('VariantSurvival'), + id="nav", + windowTitle ="VariantSurvival", + tabPanel("Select Target Gene", + sidebarLayout( + sidebarPanel( h3("Annotate your data"), + pickerInput(inputId ="disease_n", + label = "Select the disease of interest:", + choices = c(colnames(disease_gene), "N/A"), + selected = "N/A" + ), + selectInput(inputId = "ids", + label = "Select the participant ID:", + choices = c(colnames(metadata), "N/A"), + selected = "N/A" + ), + selectInput(inputId = "time", + label = "Select the time factor:", + choices = c(colnames(metadata), "N/A"), + selected = "N/A" + ), + radioButtons(inputId = "time_unit", + label = "Time factor unit:", + choices = c("years", "days"), + inline = TRUE + ), + + span(shiny::tags$i( + h6("The following selections must refer to binary factors")), + style="color:#045a8d"), + selectInput(inputId = "group", + label = "Select the clinical trial groups factor:", + choices =c(colnames(metadata), "N/A"), + selected = "N/A" + ), + selectInput(inputId = "event", + label = "Select the alive/dead factor:", + choices = c(colnames(metadata), "N/A"), + selected = "N/A" + ) + ), + mainPanel( + fluidRow(width = 12, + tabBox(width = 11, + selected="All Disease Biomarkers", + tabPanel("All Disease Biomarkers", + h4("The Biomarkers table resumes the Biomarkers associated + with the diseases based on the ClinGen database"), + shinycssloaders::withSpinner(DT::dataTableOutput("biomarkers_table")) + + ), + tabPanel("Structural Variants in all Biomarkers", + shinycssloaders::withSpinner(DT::dataTableOutput("summ_table")) + ) + ) + ) + + + ) + ), + br(),br(), + sidebarLayout( + sidebarPanel( + h3("Select Target Gene"), + selectInput(inputId = "target_gene", + label = "List of biomarkers:", + choices = NULL, + selected = FALSE + ) + ), + mainPanel( + fluidRow(width = 12, + tabBox(width = 11, + selected="Structural Variants in Selected Biomarker", + + tabPanel("Structural Variants in Selected Biomarker", + + shinycssloaders::withSpinner(DT::dataTableOutput("gene_summary_table_i")), + shinycssloaders::withSpinner( DT::dataTableOutput("gene_summary_table")) + + ), + tabPanel("Structural Variants distribution ", + tabBox(selected= "Histogram", width = 11, + tabPanel( "Histogram", + #h4("Histogram Structural Variants distribution"), + shinycssloaders::withSpinner( + plotOutput(outputId = "histogram")) + ), + + tabPanel( "Table", + selectInput(inputId = "table_cols", + label = "Include columns (optional)", + choices = NULL, selected = FALSE, + multiple = TRUE), + shinycssloaders::withSpinner(DT::dataTableOutput("table")) + ) + ) + + ) + ) + ) + ) + ) + ), + tabPanel("Kaplan–Meier", + shinyjs::useShinyjs(), + tabBox( + tabPanel("Null model", + fluidRow(column(12, + div(style = "height:70px; Topleft"), + shinycssloaders::withSpinner( + plotOutput(outputId = "null_model_km"))) + ), + fluidRow(column(12, + div(style = "height:200px; Bottomleft"), + checkboxInput("life_table_null_model", + "Display life table", + value = FALSE), + box(id = "myBox", title = "", width = '200px', + span(DT::dataTableOutput("null_model_life_table")))) + ) + ), + tabPanel("Multiple model", + fluidRow(column(12, + div(style = "height:70px; Topleft"), + dropdownButton( + checkboxInput("all_n_svs", + "Include all counts", + value = TRUE + ), + selectInput(inputId = "n_svs_min", + label = "min", + choices = NULL, + selected = FALSE + ), + selectInput(inputId = "n_svs_max", + label = "max", + choices = NULL, + selected = FALSE + ), + checkboxGroupInput("km_feat", + "Plot layout options:", + choices = c("confidence interval" = "conf_itv", + "risk table" = "risk_table", + "y grid line" = "grid_line")), + circle = TRUE, + status = "danger", + icon = icon("gear"), width = "300px", + tooltip = tooltipOptions(title = "Click to see inputs !") + ), + shinycssloaders::withSpinner( + plotOutput(outputId = "plot_km",width = "100%")) + ) + ), + fluidRow(column(12, + div(style = "height:200px; Bottomleft"), + checkboxInput("life_table_multiple_model", + "Display life table", + value = FALSE), + tabBox(id = "myBox_mm", title = "", width = 12, + tabPanel("with SV", + span(DT::dataTableOutput("lt_mm_0")) + ), + tabPanel("without SV", + span(DT::dataTableOutput("lt_mm_1")) + ) + ) + ) + ) + ) + ) + ),#tab + tabPanel("Cox regression", + span(shiny::tags$i( + h3("Cox regression table")), + style="color:#045a8d", + shinyjs::useShinyjs(), + # checkboxInput("cox_reg_td", + # "With time-dependent covariates", + # value = TRUE), + selectizeInput(inputId = "sel_cov", + label = "Select categorical covariate(s)", + # SV_bin is added by us, 0/1 without/with SV + choices = NULL, + selected = FALSE, + multiple = TRUE + ), + selectizeInput(inputId = "sel_cov_cont", + label = "Select numerical covariate(s)", + choices = NULL, + selected = FALSE, + multiple = TRUE + ), + selectInput(inputId = "sel_strata", + label = "Select strata covariate (optional)", + choices = NULL), + tabBox( + tabPanel("Standard model", + span(DT::dataTableOutput("summ_std")), + br(), + br(), + span(DT::dataTableOutput("prop_h_std")), + br(), + span(shiny::tags$i( + h2("Residuals"))), + shinycssloaders::withSpinner( + plotOutput(outputId = "residues_std")) + + ), + tabPanel("Multiple model", + tabBox(width = 12, + tabPanel("with SV", + span(DT::dataTableOutput("summ_mm_1")), + br(), + br(), + tabPanel("with", + span(DT::dataTableOutput("prop_h_mm0")), + br(), + span(shiny::tags$i(h2("Residuals"))), + shinycssloaders::withSpinner(plotOutput(outputId = "residues_std_mm0")) + ), + br()), + tabPanel("without SV", + span(DT::dataTableOutput("summ_mm_0")), + br(), + br(), + tabPanel("without", + span(DT::dataTableOutput("prop_h_mm1")), + br(), + span(shiny::tags$i(h2("Residuals"))), + shinycssloaders::withSpinner(plotOutput(outputId = "residues_std_mm1")) + ) + ) + ) + ) + ) + ) + ) + ) + ) + + + server <- function(input, output, session) { + + # get disease_n input and update the genes list accordingly + observeEvent(input$disease_n, { + if(input$disease_n!= "N/A"){ + genes_list <- c(get_disease_gene_list(disease_gene,input$disease_n)) + disease_genes_names <- gene_ids_table$GeneName + updateSelectizeInput(session, + input = "target_gene", + choices = genes_list, + selected = NULL) + output$biomarkers_table <- DT::renderDataTable({ + disease_type_gene <- disease_type_gene %>% filter(disease_type_gene$GCEP ==input$disease_n ) + disease_type_gene <-unique( disease_type_gene[,-c(2,4,6,9)]) + disease_type_gene %>% arrange(DISEASE_LABEL) + df <- disease_type_gene[,-c(6)] + df + }) + } + }) + observe({ if(input$disease_n != "N/A" + & input$ids != "N/A" + &input$time != "N/A"){ + count_table<- genesCountTable(vcf, metadata, input, gene_ids_table) + output$summ_table <- DT::renderDataTable({ + # count dataframe with patient_ids in rows and gene_ids in columns + count_table + }) + } + }) + + reactive_no_NAs_metadata <- reactive({ + if(checkInput(input)){ + disease_genes_names <- gene_ids_table$GeneName + sample_names <- colnames(vcf@gt)[-1] # ignore VCF genotype information + # genes are repeated since a single gene can have more than one SV. + genes_with_svs_in_sample <- apply(vcf@fix, + 1, + getGeneName, + gene_ids_table) + # count dataframe with patient_ids in rows and gene_ids in columns + count_df <- CountSVsDf(length(disease_genes_names), + length(sample_names), + disease_genes_names, + sample_names, + genes_with_svs_in_sample, + vcf, + input$ids) + new_md <- (RemoveNAs(metadata, input$time) + %>% rename(ids = input$ids, + trial_group_bin = input$group, + time = input$time, + event = input$event) + ) + # what happen if the input$target_gene is not in the vcf file? + new_df <- (subset(count_df, ids %in% new_md$ids) + %>% rename(SV_count_per_gene = input$target_gene) + ) + no_na_df <- merge(new_df, new_md, by = "ids") + no_na_df <- transform(no_na_df, + time = as.numeric(time), + event = as.numeric(event), + SV_count_per_gene = as.numeric(SV_count_per_gene) + ) + no_na_df <- (no_na_df + %>% mutate(SV_bin = ifelse(new_df$SV_count_per_gene>0, 1, 0) + ) + %>% mutate(trial_group = ifelse(trial_group_bin=="0", + "Placebo", + "Treatment") + ) + %>% mutate(SV = ifelse(SV_bin=="0", "with", "without") + ) + ) + if(input$time_unit == 'years'){ + no_na_df$time_days <- floor(no_na_df[["time"]] * days_year) + } else{ + no_na_df$time_years <- no_na_df[["time"]] / days_year + } + no_na_df + } + } + ) + observe({ + if(checkInput(input)){ + new_df <- reactive_no_NAs_metadata() + count_tab<- genesCountTable(vcf, metadata, input, gene_ids_table) + target_gene_df <- new_df[,c("SV_count_per_gene", "trial_group_bin")] + # subset the count of structural variants in the control/treatment patients + control <- target_gene_df$SV_count_per_gene[target_gene_df$trial_group_bin == 0] + treatment <- target_gene_df$SV_count_per_gene[target_gene_df$trial_group_bin == 1] + number_of_patients <- (count_tab + %>% filter(count_tab$Gene_ID == input$target_gene) + %>% select(`Count of patients with SVs`)) + # if(number_of_patients$`Count of patients with SVs` == 0){ + # output$gene_summary_table <- DT::renderDataTable({ + # print(dplyr::datatable("No patient carries structural variants in this gene")) + # }) + # output$gene_summary_table_i <- DT::renderDataTable({ + # print(dplyr::tibble("No patient carries structural variants in this gene")) + # }) + # } + # else{ + output$gene_summary_table <- DT::renderDataTable({ + sketch = htmltools::withTags(table( + class = 'display', + thead(tr(th(rowspan = 2, 'Group'), + th(colspan = 2, 'Number of patients') + ), + tr( + lapply(rep(c('Min', 'Max'), 1), th) + ) + ) + )) + rows_names <-c('control', 'treatment') + first_column <- c(min(control), min(treatment)) + second_column <- c(max(control), max(treatment)) + df <- data.frame(rows_names, first_column, second_column) + datatable(df, container = sketch, rownames = FALSE,options = list(dom = 't')) + }) + output$gene_summary_table_i <- DT::renderDataTable({ + sketch = htmltools::withTags(table( + class = 'display', + thead( + tr(th(rowspan = 2, 'Group'), + th(colspan = 2, 'Patients with SVs in target gene') + ), + tr(lapply(rep(c('Total', 'Percentage over entire sample'), 1), th) + ) + ) + ) + ) + rows_names <-c('control', 'treatment') + length(control[control>0]) + control <- target_gene_df$SV_count_per_gene[target_gene_df$trial_group_bin == 0] + treatment <- target_gene_df$SV_count_per_gene[target_gene_df$trial_group_bin == 1] + + n_control <- length(control[control>0]) + n_trearment <- length(treatment[treatment>0]) + n_indiv <- nrow(target_gene_df) + first_column <- c(n_control, n_trearment) + second_column <- c(round(n_control/n_indiv, 2), round(n_trearment/n_indiv, 2)) + + df <- data.frame(rows_names, first_column, second_column) + datatable(df, container = sketch, rownames = FALSE,options = list(dom = 't')) + }) + # } + } + }) + + ## output - histogram ## + output$histogram <- renderPlot( + { + if(checkInput(input)){ + new_df <- reactive_no_NAs_metadata() + # get a dataframe with counts + svs_gene_input_df <- new_df[c("ids", "trial_group", "SV_count_per_gene")] + legend_title <- "Group" + ggplot(svs_gene_input_df, aes(SV_count_per_gene, fill=trial_group)) + + geom_histogram(binwidth=1) + + stat_bin(binwidth=1, + geom='text', + color='white', + aes(label=after_stat(if_else(condition = count>0, + as.character(count), ""))), + position=position_stack(vjust = 0.5)) + + xlab("Number of SVs in target gene") + ylab("Frequency") + + theme(text = element_text(size = 20), + panel.background = element_rect(fill = "white", + colour = "white"), + axis.line = element_line(colour = "black"), + panel.grid.major = element_blank(), + panel.grid.minor = element_blank(), + legend.position="top" + ) + + scale_fill_manual(legend_title, values=c("#8B1D4D", "#5275A6")) + } + }, + height = 500, + width = 700 + ) + + observe({ + if(checkInput(input) & !is.null(input$target_gene)){ + svs_gene_input_df <- reactive_no_NAs_metadata() + # renaming back to original column names, so it's not confusing for the user. + # maybe not the best approach + rename_cols <- c("ids", "trial_group_bin", "time", "event") + rename_cols_with <- c(input$ids, input$group, input$time, input$event) + names(svs_gene_input_df)[names(svs_gene_input_df) %in% rename_cols]<- rename_cols_with + coln_list <- colnames(svs_gene_input_df) + coln_list <- coln_list[!(coln_list %in% c(input$ids,"SV_count_per_gene"))] + updateSelectizeInput(session, + input = "table_cols", + choices = coln_list, + selected = NULL) + } + }) + + observe({ + if(checkInput(input)){ + svs_gene_input_df <- reactive_no_NAs_metadata() + # renaming back to original column names, so it's not confusing for the user. + # maybe not the best approach + rename_cols <- c("ids", "trial_group_bin", "time", "event") + rename_cols_with <- c(input$ids, input$group, input$time, input$event) + names(svs_gene_input_df)[names(svs_gene_input_df) %in% rename_cols]<- rename_cols_with + if(any(!is.na(input$table_cols))){ + output$table <- DT::renderDataTable({ + col_names_list <- c(c(input$ids, "SV_count_per_gene"), + input$table_cols) + svs_gene_input_df <- as_tibble(svs_gene_input_df[col_names_list]) + svs_gene_input_df + }) + } + else{ + output$table <- DT::renderDataTable({ + svs_gene_input_df <- as_tibble(svs_gene_input_df[c(input$ids, "SV_count_per_gene")]) + colnames(svs_gene_input_df) <- c("ID", "SV count in gene of interest") + svs_gene_input_df + }) + } + } + }) + + observe({ + if(checkInput(input)){ + svs_gene_input_df <- reactive_no_NAs_metadata() + null_model <- survfit(Surv(time, event)~1, + data = svs_gene_input_df, + type = "kaplan-meier") + output$null_model_km <- renderPlot({ + ggsurvplot_combine(list(null_model), + data=no_na_df, + risk.table = FALSE, + conf.int = FALSE, + conf.int.style = "step", + risk.table.y.text = FALSE, + xlab = "Years", + ylab = "Overall survival probability", + legend = "none", + ggtheme = theme( + text = element_text(size = 20), + panel.background = element_rect(fill = "white", + colour = "white"), + axis.line = element_line(colour = "black"), + panel.grid.major.y = element_line(colour='white'), + panel.grid.minor.y = element_line(colour='white'), + # legend.position = c(0.2, 0.5) + )) + }, + height = 500, + width = 700) + + observeEvent(input$life_table_null_model, { + if(input$life_table_null_model == FALSE){ + shinyjs::hide(id = "myBox") + } + else if(input$life_table_null_model==TRUE){ + shinyjs::show(id = "myBox") + output$null_model_life_table <- DT::renderDataTable({ + as_tibble(round_df(as.data.frame(surv_summary(null_model)), 3)) + }) + } + }) + } + }) + + observe({ + if(checkInput(input)){ + risk_table = FALSE + conf_itv = FALSE + grid_line = "white" + if(!is.null(input$km_feat)){ + if("conf_itv" %in% input$km_feat){ + conf_itv = TRUE} + if("risk_table" %in% input$km_feat){ + risk_table = TRUE} + if("grid_line" %in% input$km_feat){ + grid_line = "grey"} + } + svs_gene_input_df <- reactive_no_NAs_metadata() + if (input$all_n_svs == FALSE + & input$n_svs_min!= "" + & input$n_svs_max!= ""){ + if (input$n_svs_max > input$n_svs_min){ + n_svs_min = as.numeric(input$n_svs_min) + n_svs_max = as.numeric(input$n_svs_max) + sub <- (svs_gene_input_df$SV_count_per_gene >= n_svs_min + & svs_gene_input_df$SV_count_per_gene <= n_svs_max) + svs_gene_input_df <- svs_gene_input_df[sub,] + } + } + groups_df <- (unique(svs_gene_input_df[c("SV_bin", "trial_group_bin")]) + %>% arrange(SV_bin, trial_group_bin)) + lables <- c() + cols <- c() + for (row in 1:nrow(groups_df)){ + sv_bin <- groups_df[row, "SV_bin"] + trial_g <- groups_df[row, "trial_group_bin"] + if (sv_bin == 0){ + if (trial_g == 0){ + lables <- c(lables, "without sv - placebo") + cols <- c(cols, "Violetred2") + } + else if (trial_g == 1){ + lables <- c(lables, "without sv - treatment") + cols <- c(cols, "turquoise3") + } + } + if (sv_bin == 1){ + if (trial_g == 0){ + lables <- c(lables, "with sv - placebo") + cols <- c(cols, "Violetred4") + } + else if (trial_g == 1){ + lables <- c(lables, "with sv - treatment") + cols <- c(cols, "steelblue") + } + } + } + n_sv_groups <- unique(svs_gene_input_df[["SV_bin"]]) + # can it happen that there are more than 1 patient groups? + if(length(n_sv_groups) == 2){ + # generate survival curve objects for each group + sc_without <- survfit2(Surv(time, event)~trial_group_bin, + data = svs_gene_input_df, + subset=(SV_bin==0), + type = "kaplan-meier") + sv_with <- survfit2(Surv(time, event)~trial_group_bin, + data = svs_gene_input_df, + subset=(SV_bin==1), + type = "kaplan-meier") + surv_fit_list <- list("with SV" = sv_with, "without SV" = sc_without) + } + else if(length(n_sv_groups) ==1){ + if (n_sv_groups == 0){ + type = "without"} + else if (n_sv_groups == 1){ + type = "with"} + temp <- paste(type , " SV") + sc <- survfit2(Surv(time, event)~trial_group_bin, + data = svs_gene_input_df, + type = "kaplan-meier") + surv_fit_list <- list(temp = sc) + } + + output$plot_km <- renderPlot({ + ggsurvplot_combine(surv_fit_list, + data=svs_gene_input_df, + risk.table = risk_table, + conf.int = conf_itv, + conf.int.style = "step", + risk.table.y.text = FALSE, + xlab = toTitleCase(input$time_unit), + ggtheme = theme( + text = element_text(size = 20), + panel.background = element_rect(fill = "white", + colour = "white"), + axis.line = element_line(colour = "black"), + panel.grid.major.y = element_line(colour=grid_line), + panel.grid.minor.y = element_line(colour=grid_line), + # legend.position = c(0.2, 0.5) + ), + legend = "right", + legend.title = "Group", + legend.labs =lables, + palette = cols + )}, + height = 600, + width = 1000) + + observeEvent(input$life_table_multiple_model, { + if(input$life_table_multiple_model == FALSE){ + shinyjs::hide(id = "myBox_mm") + } + else if(input$life_table_multiple_model==TRUE){ + shinyjs::show(id = "myBox_mm") + output$lt_mm_0 <- DT::renderDataTable({ + tl_sv_without <- data.frame(lapply(surv_summary(sc_without, data = svs_gene_input_df), + function(x) if(is.numeric(x)) round(x, 3) else x)) + tl_sv_without <- tl_sv_without[, !names(tl_sv_without) %in% c("strata")] + as_tibble(tl_sv_without) + }) + output$lt_mm_1 <- DT::renderDataTable({ + tl_sv_with <- data.frame(lapply(surv_summary(sv_with, data = svs_gene_input_df), + function(x) if(is.numeric(x)) round(x, 3) else x)) + tl_sv_with <- tl_sv_with[, !names(tl_sv_with) %in% c("strata")] + as_tibble(tl_sv_with) + }) + } + }) + } + else{ + output$plot_km <- renderText({ "Missing input data"}) + } + }) +########################### COX ############################### +################################################################################## + inputs_react <- reactive({list(input$event, + input$time, + input$ids, + input$target_gene + )}) + # hide the event, time and ids covariates from the covariates and strata + # drop-down + observeEvent(inputs_react(),{ + if(checkInput(input)){ + svs_gene_input_df <- reactive_no_NAs_metadata() + svs_levels <- unique(svs_gene_input_df["SV_count_per_gene"])$SV_count_per_gene + cov_list <- c(get_cov_list(metadata, input), "SV_bin") + # update the covariate drop down + updateSelectizeInput(session, + input = "sel_cov", + choices = cov_list, + options = list(create = TRUE)) + # update the strata drop down, this field is optional + updateSelectizeInput(session, + input = "sel_cov_cont", + choices = cov_list, + options = list(create = TRUE)) + updateSelectizeInput(session, + input = "sel_strata", + choices = c(cov_list, c("SV_bin","N/A")), + selected = "N/A") + } + } + ) + + observeEvent(input$all_n_svs, { + if (checkInput(input)){ + if (input$all_n_svs == FALSE){ + shinyjs::enable("n_svs_min") + shinyjs::enable("n_svs_max") + svs_gene_input_df <- reactive_no_NAs_metadata() + svs_levels <- unique(svs_gene_input_df["SV_count_per_gene"])$SV_count_per_gene + updateSelectizeInput(session, + input = "n_svs_min", + choices = sort(svs_levels)) + } + else { + shinyjs::disable("n_svs_min") + shinyjs::disable("n_svs_max") + } + } + } + ) + + observeEvent(input$n_svs_min, { + if (checkInput(input)){ + if (input$all_n_svs == FALSE & input$n_svs_min!=""){ + svs_gene_input_df <- reactive_no_NAs_metadata() + svs_levels <- unique(svs_gene_input_df["SV_count_per_gene"])$SV_count_per_gene + max_levels <- sort(svs_levels[svs_levels >= as.numeric(input$n_svs_min)]) + updateSelectizeInput(session, input = "n_svs_max", choices = max_levels) + } + } + } + ) + + observe({ + if(checkInput(input) & (any(!is.na(input$sel_cov)) | any(!is.na(input$sel_cov_cont)))){ + covariates <- c() + input_df <- reactive_no_NAs_metadata() + if (any(!is.na(input$sel_cov_cont))){ + input_cov_cont <- map_col_names(input, input$sel_cov_cont) + input_df[input_cov_cont] <- sapply(input_df[input_cov_cont],as.numeric) + covariates <- c(covariates, input_cov_cont) + } + if(any(!is.na(input$sel_cov))){ + input_cov_cat <- map_col_names(input, input$sel_cov) + input_df[input_cov_cat] <- sapply(input_df[input_cov_cat],as.character) + covariates <- c(covariates, input_cov_cat) + } + if(input$sel_strata != "N/A"){ + covariates <- c(covariates[covariates != input$sel_strata], sprintf("strata(%s)", input$sel_strata)) + } + # Standard model + formulaString <- paste("Surv(time, event) ~", paste(covariates, collapse="+")) + cox_reg.std <- coxph(as.formula(formulaString), data=input_df) + ## Check for violation of proportional hazard + res.std <- cox.zph(cox_reg.std) + + # here + output$summ_std <- DT::renderDataTable({ + as_tibble(cox_reg.std %>% tbl_regression(exp = TRUE)) + }) + output$prop_h_std <- DT::renderDataTable({ + datatable(rownames_to_column(round_df(as.data.frame(res.std$table),3), " "), + options = list(dom = 't')) + }) + output$residues_std <- renderPlot({ + par(mfrow=c(length(covariates),1)) + plot(res.std) + }) + ######################################" + # Multiple model + input_df_mm <- data.frame(input_df) + input_df_mm["SV_bin"] <- sapply(input_df_mm["SV_bin"], as.numeric) + formulaString_mm <- paste("Surv(time, event) ~", paste(covariates[!(covariates %in% c("SV_bin", "strata(SV_bin)"))], collapse="+")) + # + cox_reg.mul0 <- coxph(as.formula(formulaString_mm), + data=input_df_mm, + subset=(SV_bin==0)) + res.std_mul0 <- cox.zph(cox_reg.mul0) + # + output$summ_mm_0 <- DT::renderDataTable({ + as_tibble(cox_reg.mul0 %>% tbl_regression(exp = TRUE)) + }) + output$prop_h_mm0 <- DT::renderDataTable({ + datatable(rownames_to_column(round_df(as.data.frame(res.std_mul0$table),3), " "), + options = list(dom = 't')) + }) + output$residues_std_mm0 <- renderPlot({ + par(mfrow=c(length(covariates),1)) + plot(res.std_mul0) + }) + # ERROR: Warning: Error in coxph: No (non-missing) observations + #cox_reg.mul1 <- coxph(as.formula(formulaString_mm), + # data=input_df_mm, + # subset=(SV_bin==1)) + #res.std_mul1 <- cox.zph(cox_reg.mul1) + #output$summ_mm_1 <- DT::renderDataTable({ + # as_tibble(cox_reg.mul1 %>% tbl_regression(exp = TRUE)) + #}) + #output$prop_h_mm1 <- DT::renderDataTable({ + # datatable(rownames_to_column(round_df(as.data.frame(res.std_mul1$table),3), " "), + # options = list(dom = 't')) + #}) + output$residues_std_mm1 <- renderPlot({ + par(mfrow=c(length(covariates),1)) + plot(res.std_mul1) + }) + + } + }) + + } + + # Run the application + shinyApp(ui = ui, server = server) + +} + +#' implementation of += operator +#' https://stackoverflow.com/questions/5738831/ +#' @noRd +`%+=%` <- function(e1,e2) eval.parent(substitute(e1 <- e1 + e2)) diff --git a/variantsurvival/R/checkInput.R b/variantsurvival/R/checkInput.R new file mode 100644 index 0000000..30d5046 --- /dev/null +++ b/variantsurvival/R/checkInput.R @@ -0,0 +1,15 @@ +#' `checkInput` +#' @param info info +#' @return true or false +#' @noRd +checkInput <- function(input) { + if (input$ids != "N/A" + & input$time != "N/A" + & input$group != "N/A" + & input$event != "N/A" + & input$target_gene != "N/A"){ + return(TRUE) + }else{ + return(FALSE) + } +} diff --git a/variantsurvival/R/genesCountTable.R b/variantsurvival/R/genesCountTable.R new file mode 100644 index 0000000..f9f17f0 --- /dev/null +++ b/variantsurvival/R/genesCountTable.R @@ -0,0 +1,29 @@ +#' genesCountTable +#' +#' @param vcf file +#' @param metadata file +#' @param input input +#' @param gene_ids_table table +#' @noRd +#' @return count_table +genesCountTable <- function(vcf, metadata, input, gene_ids_table){ + genes_with_svs_in_sample <- apply(vcf@fix, 1, getGeneName, gene_ids_table) + sample_names <- colnames(vcf@gt)[-1] + disease_genes_names <- gene_ids_table$GeneName + count_df <- CountSVsDf(length(disease_genes_names), + length(sample_names), + disease_genes_names, + sample_names, + genes_with_svs_in_sample, + vcf, + input$ids) + new_md <- RemoveNAs(metadata, input$time) %>% rename(ids = input$ids) + # what happen if the input$target_gene is not in the vcf file? + new_df <- subset(count_df, ids %in% new_md$ids) + ## + count_table <- as.data.frame(apply(new_df[,-1], 2, function(c)sum(c!=0))) + colnames(count_table) <- "Count of patients with SVs" + count_table <- rownames_to_column(count_table, "Gene_ID") + count_table <- count_table %>% arrange(desc(count_table["Count of patients with SVs"])) + return(count_table) +} diff --git a/variantsurvival/R/getGeneName.R b/variantsurvival/R/getGeneName.R new file mode 100644 index 0000000..a2414d7 --- /dev/null +++ b/variantsurvival/R/getGeneName.R @@ -0,0 +1,8 @@ +#' `getGeneName` +#' @param info info +#' @return gene id +#' @noRd +getGeneName <- function(info, geneIDS) { + x <- str_extract(info['INFO'], "(?<=ensembl_gene_id=)[^;]+") + return(geneIDS[x,]$GeneName) +} diff --git a/variantsurvival/R/get_cov_list.R b/variantsurvival/R/get_cov_list.R new file mode 100644 index 0000000..4cec8c4 --- /dev/null +++ b/variantsurvival/R/get_cov_list.R @@ -0,0 +1,13 @@ +#' get_cov_list +#' +#' @param metadata file +#' @param input file +#' @noRd +#' @return cov_list + +get_cov_list <- function(metadata, input) { + inputs_list <- c(input$event, input$time, input$ids) + cov_list <- colnames(metadata) + cov_list <- cov_list[!(cov_list %in% inputs_list)] + return(cov_list) +} diff --git a/variantsurvival/R/get_disease_gene_list.R b/variantsurvival/R/get_disease_gene_list.R new file mode 100644 index 0000000..13c0e05 --- /dev/null +++ b/variantsurvival/R/get_disease_gene_list.R @@ -0,0 +1,11 @@ +#' `get_disease_gene_list` parses an existing .txt +#' file containing all known target genes associated +#' with the selected disease. +#' @param input_disease: input disease selection +#' @return genes_list +#' @noRd +get_disease_gene_list <- function(disease_gene, input_disease) { + genes_list <-( na.omit(disease_gene[,input_disease]) + %>% rename(genes = input_disease)) + return(genes_list$genes) +} diff --git a/variantsurvival/R/load.R b/variantsurvival/R/load.R new file mode 100644 index 0000000..6835a53 --- /dev/null +++ b/variantsurvival/R/load.R @@ -0,0 +1,44 @@ +#' load +#' @noRd + + +load <- function() { + if (!require("shiny")) install.packages("shiny") + if (!require("shinyjs")) install.packages("shinyjs") + if (!require("shinyWidgets")) install.packages("shinyWidgets") + if (!require("shinythemes")) install.packages("shinythemes") + if (!require("shinycssloaders")) install.packages("shinycssloaders") + if (!require("shinydashboard")) install.packages("shinydashboard") + if (!require("DT")) install.packages("DT") + if (!require("dplyr")) install.packages("dplyr") + if (!require("tidyverse")) install.packages("tidyverse") + if (!require("vcfR")) install.packages("vcfR") + if (!require("readr")) install.packages("readr") + if (!require("ggsurvfit")) install.packages("ggsurvfit") + if (!require("survival")) install.packages("survival") + if (!require("ggplot2")) install.packages("ggplot2") + if (!require("survminer")) install.packages("survminer") + if (!require("lubridate")) install.packages("lubridate") + if (!require("gtsummary")) install.packages("gtsummary") + if (!require("tools")) install.packages("tools") + library(tools) + library(shiny) + library(shinyjs) + library(shinydashboard) + library(shinythemes) + library(shinyWidgets) + library(shinycssloaders) + library(DT) + library(dplyr) + library(tidyverse) + library(vcfR) + library(readr) + library(readxl) + library(ggsurvfit) + library(survival) + library(ggplot2) + library(survminer) + library(lubridate) + library(gtsummary) + +} diff --git a/variantsurvival/R/map_col_names.R b/variantsurvival/R/map_col_names.R new file mode 100644 index 0000000..e9e1b67 --- /dev/null +++ b/variantsurvival/R/map_col_names.R @@ -0,0 +1,18 @@ +#' map_col_names +#' +#' @param input input +#' @param cov_list list +#' @noRd +#' @return cov_list +map_col_names <- function(input, cov_list){ + if(input$event %in% cov_list){ + cov_list <- str_replace(cov_list, + input$event, + "event")} + if(input$group %in% cov_list){ + cov_list <- str_replace(cov_list, + input$group, + "trial_group_bin") + } + return(cov_list) +} diff --git a/variantsurvival/R/round_df.R b/variantsurvival/R/round_df.R new file mode 100644 index 0000000..3c262cb --- /dev/null +++ b/variantsurvival/R/round_df.R @@ -0,0 +1,12 @@ +#' round_df +#' round all numeric variables +#' @param x data frame +#' @param digits number of digits to round +#' @noRd +#' @return x + +round_df <- function(x, digits) { + numeric_columns <- sapply(x, mode) == 'numeric' + x[numeric_columns] <- round(x[numeric_columns], digits) + x +} diff --git a/variantsurvival/R/sysdata.rda b/variantsurvival/R/sysdata.rda new file mode 100644 index 0000000..a92cf3b Binary files /dev/null and b/variantsurvival/R/sysdata.rda differ diff --git a/VariantSurvival_package/VariantSurvival.Rproj b/variantsurvival/VariantSurvival.Rproj similarity index 100% rename from VariantSurvival_package/VariantSurvival.Rproj rename to variantsurvival/VariantSurvival.Rproj diff --git a/VariantSurvival_package/man/VariantSurvival.Rd b/variantsurvival/man/VariantSurvival.Rd similarity index 82% rename from VariantSurvival_package/man/VariantSurvival.Rd rename to variantsurvival/man/VariantSurvival.Rd index 4c4403c..0c14e6b 100644 --- a/VariantSurvival_package/man/VariantSurvival.Rd +++ b/variantsurvival/man/VariantSurvival.Rd @@ -4,12 +4,14 @@ \alias{VariantSurvival} \title{VariantSurvival} \usage{ -VariantSurvival(vcffile, metadatafile) +VariantSurvival(vcffile, metadatafile, demo = FALSE) } \arguments{ \item{vcffile}{path to the vcf file containing the Structural variant data} \item{metadatafile}{path to the txt file containing the samples metadata} + +\item{demo}{true or false} } \description{ VariantSurvival