Some text, plots and tables from a NBIS user-fee project
+
+
+
+
+
+
+
+
Author
+
+
Verena Kutschera
+
+
+
+
+
Published
+
+
May 14, 2024
+
+
+
+
+
+
+
+
+
+
+
+
+
Data
+
+
Library construction and sequencing (from NGI report)
+
Libraries were construction using the Illumina TruSeq PCR-free library prep kit. Samples were sequenced on NovaSeq6000 in a ‘S4’ mode flowcell. Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite.
+
+
Raw data location on Rackham: /proj/snic2020-X-XXX/private/DataDelivery_2023-XX-XX_XX-XX-XX_ngisthlm00XXX/files/PXXXXX
+
+
Please note that NBIS recommends to submit raw data to ENA as soon as possible
+
+
+
+
+
+Table 1: Sample metadata
+
+
+
+
+
+
Sample_ID
+
NGI_ID
+
Mreads
+
>=Q30
+
Date
+
Sex
+
+
+
+
+
F34
+
PXXXXX_113
+
109.65
+
90.04
+
2022
+
F
+
+
+
F41
+
PXXXXX_114
+
119.48
+
89.87
+
2022
+
M
+
+
+
F42
+
PXXXXX_115
+
91.88
+
89.91
+
2022
+
F
+
+
+
F43
+
PXXXXX_116
+
106.51
+
89.93
+
2022
+
F
+
+
+
F44
+
PXXXXX_117
+
112.15
+
89.75
+
2022
+
M
+
+
+
O1
+
PXXXXX_101
+
110.42
+
89.80
+
2022
+
M
+
+
+
O11
+
PXXXXX_203
+
136.61
+
90.22
+
2022
+
M
+
+
+
O15
+
PXXXXX_107
+
110.25
+
89.98
+
2022
+
M
+
+
+
O16
+
PXXXXX_108
+
102.67
+
89.62
+
2022
+
F
+
+
+
+
+
+
+
Sample_ID: sample identifier used for sampling and laboratorywork. NGI_ID: NGI sample identifier, Mreads:total millionread pairs for a sample,>=Q30: aggregated percentage of basesthat have a quality score >= Q30, Longitude / Latitude:geographic sampling location, Date: sampling year,Sex: M=male, F=female
+
+
+
+
Some methods
+
+
Whole-genome sequencing data processing
+
Whole-genome sequencing data from nine individuals (Table 1) were processed and analysed using GenErode v0.6.0 (Kutschera et al. 2022) with default settings if not otherwise described.
+
+
+
+
Some results
+
+
Population structure
+
FST was calculated in 50 kb windows between island and mainland samples. The mean FST across all 50 kb windows (with zero missing data allowed) was 0.036.
+
+
+Code
+
import os
+import pandas as pd
+import numpy as np
+
+def mean_fst(fst_file):
+ fst_df = pd.read_table(fst_file, delim_whitespace=True, header=0)
+ mean_fst = fst_df['MEAN_FST'].mean()
+print(mean_fst)
+
+fst ="windowed.weir.fst"
+
+mean_fst(fst)
+
+
+
0.03610024109357622
+
+
+
+
+
Genome-wide heterozygosity
+
We estimated individual heterozygosity calculated as the number of heterozygote sites (i.e., SNPs) per site (theta = 4Neμ) using mlRho.
+
+
+Code
+
import pandas as pd
+import scipy.stats as stats
+
+def mlRho_dataframe(inputfiles):
+# define a function to get the input data
+ dataframes = []
+for infile in inputfiles:
+ dataset =str(infile).split(".")[0]
+withopen(infile) as f:
+for i in f: # create one dataframe per input file
+ path_list = i.split("/")
+ sample = path_list[-1].split(".")[0]
+ genomeregion = path_list[-1].split(".")[-3]
+if genomeregion =="genome":
+ genomeregion ="genomewide"
+elif genomeregion =="autos":
+ genomeregion ="autosomes"
+elif genomeregion =="sexchr":
+ genomeregion ="sexchromosomes"
+ sample_df=pd.read_table(i.strip(), delim_whitespace=True, comment='#')
+ sample_df.insert(0, 'dataset', [dataset])
+ sample_df.insert(1, 'sample', [sample])
+ sample_df.insert(2, 'genomeregion', [genomeregion])
+ dataframes.append(sample_df)
+ conc_df = pd.concat(dataframes) # concatenate all dataframes
+ conc_df.reset_index(drop=True, inplace=True)
+ conc_df = conc_df.sort_values(by = ['dataset', 'sample'], ascending = [True, True])
+return conc_df
+
+def process_mlrho_dataframe(mlrho_df):
+# function to read in and process the data
+ mlrho_df['lower_theta'] = mlrho_df['theta'].str.split('<').str[0].astype(float)
+ mlrho_df['theta_est'] = mlrho_df['theta'].str.split('<').str[1].astype(float)
+ mlrho_df['upper_theta'] = mlrho_df['theta'].str.split('<').str[2].astype(float)
+ grouped_df = mlrho_df.groupby('dataset')
+return mlrho_df, grouped_df
+
+def mann_whitney_u(statistic, dataset1, list1, dataset2, list2):
+# perform Wilcoxon rank-sum test (equivalent to Mann-Whitney U test)
+print('**** Mann-Whitney U test of',statistic,'****\n')
+ stat, p_value = stats.mannwhitneyu(list1, list2)
+print('\tU=%.2f, p=%.2f'% (stat, p_value))
+
+# Level of significance
+ alpha =0.05
+# conclusion
+if p_value < alpha:
+print('\tRejecting Null Hypothesis (Significant difference between the two samples)')
+else:
+print('\tCannot Reject Null Hypothesis (No significant difference between the two samples)')
+
+print('\n\tSamples and sample sizes:\n\t', dataset1,'n =',len(list1), '\n\t', dataset2, 'n =', len(list2))
+
+# read in the data
+infiles = ['mainland.txt', 'island.txt']
+
+# apply the functions
+mlRho_df = mlRho_dataframe(infiles)
+tabledf, groupeddf = process_mlrho_dataframe(mlRho_df)
+
+listdf = tabledf.groupby('dataset')['theta_est'].apply(list)
+
+print('Mainland:')
+print('\tMedian heterozygosity %.6f'% (pd.Series(listdf['mainland']).median()))
+print('\tMinimum heterozygosity %.6f'% (pd.Series(listdf['mainland']).min()))
+print('\tMaximum heterozygosity %.6f'% (pd.Series(listdf['mainland']).max()), '\n')
+
+print('Island:')
+print('\tMedian heterozygosity %.6f'% (pd.Series(listdf['island']).median()))
+print('\tMinimum heterozygosity %.6f'% (pd.Series(listdf['island']).min()))
+print('\tMaximum heterozygosity %.6f'% (pd.Series(listdf['island']).max()), '\n')
+
+mann_whitney_u('Heterozygosity', 'Mainland', listdf['mainland'], 'Island', listdf['island'])
+
+
+
Mainland:
+ Median heterozygosity 0.000731
+ Minimum heterozygosity 0.000709
+ Maximum heterozygosity 0.000739
+
+Island:
+ Median heterozygosity 0.000695
+ Minimum heterozygosity 0.000594
+ Maximum heterozygosity 0.000737
+
+**** Mann-Whitney U test of Heterozygosity ****
+
+ U=16.50, p=0.14
+ Cannot Reject Null Hypothesis (No significant difference between the two samples)
+
+ Samples and sample sizes:
+ Mainland n = 5
+ Island n = 4
+
+
+
+
+Code
+
import matplotlib.pyplot as plt
+import pandas as pd
+from matplotlib import cm
+from matplotlib.colors import ListedColormap, LinearSegmentedColormap
+
+def theta_plot(dataframe, grouped, dataset, ax, color):
+# function for the subplots
+ data_df = grouped.get_group(dataset)
+for lower,theta,upper,x inzip(data_df['lower_theta'],data_df['theta_est'],data_df['upper_theta'],range(len(data_df))):
+ ax.plot((x,x),(lower,upper),'-',color=color)
+ ax.plot((x),(theta),'o',color=color)
+ ax.set_xticks(range(len(data_df)))
+ ax.set_xticklabels(list(data_df['sample']), rotation =45)
+
+def combine_theta_plots(dataframe, grouped):
+# function to create the combined plot
+ cividis = cm.get_cmap('cividis', 256) # create the cividis colormap
+ fig, (ax1, ax2) = plt.subplots(ncols=2, sharey=True)
+ ax1.set_xlabel("Mainland", fontsize=12)
+ ax2.set_xlabel("Island", fontsize=12)
+ theta_plot(dataframe, grouped, "mainland", ax1, cividis.colors[200])
+ theta_plot(dataframe, grouped, "island", ax2, cividis.colors[80])
+ fig.supxlabel('samples') # x axis label
+
+ fig.supylabel('theta', fontsize=12) # common y axis label
+ fig.align_labels() # align axis labels
+
+ plt.tight_layout()
+ plt.show()
+
+combine_theta_plots(tabledf, groupeddf)
+
+
+
+
+
+
+
+
+Figure 1: Genome-wide autosomal individual heterozygosity of nine individuals. Theta = 4Neμ = number of heterozygous sites per site. Error bars represent 95% confidence intervals.
+
+
+
+
+
+
+
+
+
References
+
+
+Kutschera, Verena E., Marcin Kierczak, Tom van der Valk, Johanna von Seth, Nicolas Dussex, Edana Lord, Marianne Dehasque, et al. 2022. “GenErode: A Bioinformatics Pipeline to Investigate Genome Erosion in Endangered and Extinct Species.”BMC Bioinformatics 23: 1–17. https://doi.org/10.1186/S12859-022-04757-0.
+
+ df-print: paged
+ code-fold: true
+ smooth-scroll: true
+ embed-resources: true
+ code-line-numbers: true
+ revealjs:
+ theme: [default, nbis.scss]
+ logo: nbis-logo-green.svg
+ slide-number: false
+ scrollable: true
+ embed-resources: true
diff --git a/quarto-to-wiki/quarto-example-verena/_extensions/nbis/nbis-logo-green.svg b/quarto-to-wiki/quarto-example-verena/_extensions/nbis/nbis-logo-green.svg
new file mode 100644
index 0000000..f829660
--- /dev/null
+++ b/quarto-to-wiki/quarto-example-verena/_extensions/nbis/nbis-logo-green.svg
@@ -0,0 +1,3 @@
+
+
+
\ No newline at end of file
diff --git a/quarto-to-wiki/quarto-example-verena/_extensions/nbis/nbis.scss b/quarto-to-wiki/quarto-example-verena/_extensions/nbis/nbis.scss
new file mode 100644
index 0000000..6e56576
--- /dev/null
+++ b/quarto-to-wiki/quarto-example-verena/_extensions/nbis/nbis.scss
@@ -0,0 +1,162 @@
+
+/*-- scss:defaults --*/
+
+$theme: "nbis" !default;
+
+// NBIS base colours
+$green: #92BB55 !default;
+$blue: #0093BD !default;
+$orange: #EF7C00 !default;
+
+// NBIS light colours
+$lgreen: #F8FFE5 !default;
+$lblue: #E5F9FF !default;
+$lorange: #FFF2E5 !default;
+
+// Extra colours
+$red: #BB5454 !default;
+$yellow: #BBBB54 !default;
+$purple: #AF75A7 !default;
+
+// Greyscale colours
+$white: #FFFFFF !default;
+$grey-100: #F5F5F5 !default;
+$grey-90: #E5E5E5 !default;
+$grey-80: #CCCCCC !default;
+$grey-70: #B2B2B2 !default;
+$grey-60: #999999 !default;
+$grey-50: #7F7F7F !default;
+$grey-40: #666666 !default;
+$grey-30: #4C4C4C !default;
+$grey-20: #333333 !default;
+$grey-10: #191919 !default;
+$black: #000000 !default;
+
+// Theme
+$primary: $green !default;
+$secondary: $blue !default;
+$light: $grey-100 !default;
+$dark: $grey-30 !default;
+$success: $green !default;
+$info: $purple !default;
+$warning: $yellow !default;
+$danger: $red !default;
+
+// Code
+$code-color: $primary !default;
+$code-bg: $light !default;
+$code-block-bg: $light !default;
+
+// Links
+$link-color: $primary !default;
+
+// Popover
+$popover: $light !default;
+
+// Dropdowns
+$dropdown-link-color: $grey-30 !default;
+$dropdown-link-hover-color: $white !default;
+$dropdown-link-hover-bg: $primary !default;
+
+// Fonts
+$font-family-sans-serif: Lato, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol" !default;
+$h1-font-size: 2.5rem !default;
+$h2-font-size: 2.0rem !default;
+$h3-font-size: 1.5rem !default;
+
+// Tables
+$table-bg-scale: 0 !default;
+
+// Navs
+$nav-link-padding-y: .5rem !default !default;
+$nav-link-padding-x: 2rem !default;
+$nav-link-disabled-color: $grey-40 !default !default;
+$nav-tabs-border-color: $grey-80 !default;
+
+// Navbar
+$navbar-padding-y: 1rem !default;
+$navbar-light-bg: $primary !default;
+$navbar-light-color: $white !default;
+$navbar-light-hover-color: $success !default;
+$navbar-light-active-color: $success !default;
+$navbar-light-brand-color: $white !default;
+$navbar-light-brand-hover-color: $navbar-light-brand-color !default;
+$navbar-dark-color: $white !default;
+$navbar-dark-hover-color: $primary !default;
+$navbar-dark-active-color: $primary !default;
+$navbar-dark-brand-color: $white !default;
+$navbar-dark-brand-hover-color: $navbar-dark-brand-color !default;
+
+// Pagination
+$pagination-color: $white !default;
+$pagination-bg: $success !default;
+$pagination-border-width: 0 !default;
+$pagination-border-color: transparent !default;
+$pagination-hover-color: $white !default;
+$pagination-hover-bg: darken($success, 15%) !default;
+$pagination-hover-border-color: transparent !default;
+$pagination-active-bg: $pagination-hover-bg !default;
+$pagination-active-border-color: transparent !default;
+$pagination-disabled-color: $grey-80 !default;
+$pagination-disabled-bg: lighten($success, 15%) !default;
+$pagination-disabled-border-color: transparent !default;
+
+// List group
+$list-group-hover-bg: $grey-80 !default;
+$list-group-disabled-bg: $grey-80 !default;
+
+// Close
+$btn-close-color: $white !default;
+$btn-close-opacity: .4 !default;
+$btn-close-hover-opacity: 1 !default;
+
+/*-- scss:rules --*/
+
+// Variables
+$web-font-path: "https://fonts.googleapis.com/css2?family=Lato:ital,wght@0,400;0,700;1,400&display=swap" !default;
+@if $web-font-path {
+ @import url($web-font-path);
+}
+
+// Navbar
+.bg-primary {
+ .navbar-nav .show > .nav-link,
+ .navbar-nav .nav-link.active,
+ .navbar-nav .nav-link:hover,
+ .navbar-nav .nav-link:focus {
+ color: $success !important;
+ }
+}
+
+// Navs
+.nav-tabs {
+ .nav-link.active,
+ .nav-link.active:focus,
+ .nav-link.active:hover,
+ .nav-item.open .nav-link,
+ .nav-item.open .nav-link:focus,
+ .nav-item.open .nav-link:hover {
+ color: $primary;
+ }
+}
+
+// Pagination
+.pagination {
+ a:hover {
+ text-decoration: none;
+ }
+}
+
+// Blockquotes
+.blockquote {
+ color: $lgreen;
+ border-left-color: $primary;
+}
+
+// Cell Output
+.cell-output-error > pre > code {
+ color: $red;
+}
+.cell-output-stderr > pre > code {
+ color: $yellow;
+}
diff --git a/quarto-to-wiki/quarto-example-verena/_extensions/nbis/nbis.theme b/quarto-to-wiki/quarto-example-verena/_extensions/nbis/nbis.theme
new file mode 100644
index 0000000..4e17af6
--- /dev/null
+++ b/quarto-to-wiki/quarto-example-verena/_extensions/nbis/nbis.theme
@@ -0,0 +1,211 @@
+{
+ "text-color": null,
+ "background-color": null,
+ "line-number-color": "#aaaaaa",
+ "line-number-background-color": null,
+ "text-styles": {
+ "Other": {
+ "text-color": "#9e9370",
+ "background-color": null,
+ "bold": false,
+ "italic": false,
+ "underline": false
+ },
+ "Attribute": {
+ "text-color": "#000000",
+ "background-color": null,
+ "bold": false,
+ "italic": false,
+ "underline": false
+ },
+ "SpecialString": {
+ "text-color": "#bb6688",
+ "background-color": null,
+ "bold": false,
+ "italic": false,
+ "underline": false
+ },
+ "Annotation": {
+ "text-color": "#005c86",
+ "background-color": null,
+ "bold": true,
+ "italic": true,
+ "underline": false
+ },
+ "Function": {
+ "text-color": "#0093BD ",
+ "background-color": null,
+ "bold": false,
+ "italic": false,
+ "underline": false
+ },
+ "String": {
+ "text-color": "#92BB55 ",
+ "background-color": null,
+ "bold": false,
+ "italic": false,
+ "underline": false
+ },
+ "ControlFlow": {
+ "text-color": "#9e9370",
+ "background-color": null,
+ "bold": true,
+ "italic": false,
+ "underline": false
+ },
+ "Operator": {
+ "text-color": "#666666",
+ "background-color": null,
+ "bold": false,
+ "italic": false,
+ "underline": false
+ },
+ "Error": {
+ "text-color": "#BB5454 ",
+ "background-color": null,
+ "bold": true,
+ "italic": false,
+ "underline": false
+ },
+ "BaseN": {
+ "text-color": "#EF7C00",
+ "background-color": null,
+ "bold": false,
+ "italic": false,
+ "underline": false
+ },
+ "Alert": {
+ "text-color": "#BB5454 ",
+ "background-color": null,
+ "bold": true,
+ "italic": false,
+ "underline": false
+ },
+ "Variable": {
+ "text-color": "#005c86",
+ "background-color": null,
+ "bold": false,
+ "italic": false,
+ "underline": false
+ },
+ "BuiltIn": {
+ "text-color": "#005c86",
+ "background-color": null,
+ "bold": false,
+ "italic": false,
+ "underline": false
+ },
+ "Extension": {
+ "text-color": null,
+ "background-color": null,
+ "bold": false,
+ "italic": false,
+ "underline": false
+ },
+ "Preprocessor": {
+ "text-color": "#BBBB54 ",
+ "background-color": null,
+ "bold": false,
+ "italic": false,
+ "underline": false
+ },
+ "Information": {
+ "text-color": "#005c86",
+ "background-color": null,
+ "bold": true,
+ "italic": true,
+ "underline": false
+ },
+ "VerbatimString": {
+ "text-color": "#005c86",
+ "background-color": null,
+ "bold": false,
+ "italic": false,
+ "underline": false
+ },
+ "Warning": {
+ "text-color": "#BBBB54 ",
+ "background-color": null,
+ "bold": true,
+ "italic": true,
+ "underline": false
+ },
+ "Documentation": {
+ "text-color": "#BB5454 ",
+ "background-color": null,
+ "bold": false,
+ "italic": true,
+ "underline": false
+ },
+ "Import": {
+ "text-color": "#BB5454 ",
+ "background-color": null,
+ "bold": true,
+ "italic": false,
+ "underline": false
+ },
+ "Char": {
+ "text-color": "#af75a7 ",
+ "background-color": null,
+ "bold": false,
+ "italic": false,
+ "underline": false
+ },
+ "DataType": {
+ "text-color": "#9e9370",
+ "background-color": null,
+ "bold": false,
+ "italic": false,
+ "underline": false
+ },
+ "Float": {
+ "text-color": "#EF7C00 ",
+ "background-color": null,
+ "bold": false,
+ "italic": false,
+ "underline": false
+ },
+ "Comment": {
+ "text-color": "#B2B2B2 ",
+ "background-color": null,
+ "bold": false,
+ "italic": true,
+ "underline": false
+ },
+ "CommentVar": {
+ "text-color": "#B2B2B2 ",
+ "background-color": null,
+ "bold": true,
+ "italic": true,
+ "underline": false
+ },
+ "Constant": {
+ "text-color": "#129379",
+ "background-color": null,
+ "bold": false,
+ "italic": false,
+ "underline": false
+ },
+ "SpecialChar": {
+ "text-color": "#129379",
+ "background-color": null,
+ "bold": false,
+ "italic": false,
+ "underline": false
+ },
+ "DecVal": {
+ "text-color": "#EF7C00 ",
+ "background-color": null,
+ "bold": false,
+ "italic": false,
+ "underline": false
+ },
+ "Keyword": {
+ "text-color": "#BB5454 ",
+ "background-color": null,
+ "bold": true,
+ "italic": false,
+ "underline": false
+ }
+ }
+}
diff --git a/quarto-to-wiki/quarto-example-verena/environment.yml b/quarto-to-wiki/quarto-example-verena/environment.yml
new file mode 100644
index 0000000..a7fc69f
--- /dev/null
+++ b/quarto-to-wiki/quarto-example-verena/environment.yml
@@ -0,0 +1,18 @@
+name: quarto-env
+channels:
+ - bioconda
+ - conda-forge
+dependencies:
+ - python=3.8.15
+ - biopython=1.83
+ - matplotlib=3.4.2
+ - pandas=2.0.3
+ - numpy=1.24.4
+ - jupyter
+ - r-base
+ - r-ggplot2
+ - r-rmarkdown
+ - r-reticulate
+ - nb_conda_kernels
+ - plotly
+ - scipy=1.7.0
diff --git a/quarto-to-wiki/quarto-example-verena/island.txt b/quarto-to-wiki/quarto-example-verena/island.txt
new file mode 100644
index 0000000..64b9a89
--- /dev/null
+++ b/quarto-to-wiki/quarto-example-verena/island.txt
@@ -0,0 +1,4 @@
+mlRho/O1.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
+mlRho/O11.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
+mlRho/O15.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
+mlRho/O16.merged.rmdup.merged.realn.noCpG_ref.repma.autos.mlRho.txt
\ No newline at end of file
diff --git a/quarto-to-wiki/quarto-example-verena/mainland.txt b/quarto-to-wiki/quarto-example-verena/mainland.txt
new file mode 100644
index 0000000..d24bcb1
--- /dev/null
+++ b/quarto-to-wiki/quarto-example-verena/mainland.txt
@@ -0,0 +1,5 @@
+mlRho/F34.merged.rmdup.merged.realn.noCpG_ref.repma.autos.mlRho.txt
+mlRho/F41.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
+mlRho/F42.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
+mlRho/F43.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
+mlRho/F44.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
\ No newline at end of file
diff --git a/quarto-to-wiki/quarto-example-verena/mlRho/F34.merged.rmdup.merged.realn.noCpG_ref.repma.autos.mlRho.txt b/quarto-to-wiki/quarto-example-verena/mlRho/F34.merged.rmdup.merged.realn.noCpG_ref.repma.autos.mlRho.txt
new file mode 100644
index 0000000..c885aad
--- /dev/null
+++ b/quarto-to-wiki/quarto-example-verena/mlRho/F34.merged.rmdup.merged.realn.noCpG_ref.repma.autos.mlRho.txt
@@ -0,0 +1,2 @@
+d n theta epsilon -log(L)
+0 1119932672 7.35e-04<7.37e-04<7.38e-04 1.49e-04<1.49e-04<1.49e-04 1.54e+09
diff --git a/quarto-to-wiki/quarto-example-verena/mlRho/F41.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt b/quarto-to-wiki/quarto-example-verena/mlRho/F41.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
new file mode 100644
index 0000000..8883823
--- /dev/null
+++ b/quarto-to-wiki/quarto-example-verena/mlRho/F41.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
@@ -0,0 +1,2 @@
+d n theta epsilon -log(L)
+0 1251211204 7.38e-04<7.39e-04<7.41e-04 1.42e-04<1.42e-04<1.43e-04 1.73e+09
diff --git a/quarto-to-wiki/quarto-example-verena/mlRho/F42.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt b/quarto-to-wiki/quarto-example-verena/mlRho/F42.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
new file mode 100644
index 0000000..7b345f0
--- /dev/null
+++ b/quarto-to-wiki/quarto-example-verena/mlRho/F42.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
@@ -0,0 +1,2 @@
+d n theta epsilon -log(L)
+0 1140864574 7.16e-04<7.18e-04<7.20e-04 1.37e-04<1.37e-04<1.37e-04 1.58e+09
diff --git a/quarto-to-wiki/quarto-example-verena/mlRho/F43.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt b/quarto-to-wiki/quarto-example-verena/mlRho/F43.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
new file mode 100644
index 0000000..1994e9e
--- /dev/null
+++ b/quarto-to-wiki/quarto-example-verena/mlRho/F43.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
@@ -0,0 +1,2 @@
+d n theta epsilon -log(L)
+0 1222080282 7.08e-04<7.09e-04<7.11e-04 1.32e-04<1.32e-04<1.33e-04 1.69e+09
diff --git a/quarto-to-wiki/quarto-example-verena/mlRho/F44.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt b/quarto-to-wiki/quarto-example-verena/mlRho/F44.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
new file mode 100644
index 0000000..b97d205
--- /dev/null
+++ b/quarto-to-wiki/quarto-example-verena/mlRho/F44.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
@@ -0,0 +1,2 @@
+d n theta epsilon -log(L)
+0 1201034876 7.29e-04<7.31e-04<7.32e-04 1.37e-04<1.38e-04<1.38e-04 1.66e+09
diff --git a/quarto-to-wiki/quarto-example-verena/mlRho/O1.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt b/quarto-to-wiki/quarto-example-verena/mlRho/O1.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
new file mode 100644
index 0000000..9c0589b
--- /dev/null
+++ b/quarto-to-wiki/quarto-example-verena/mlRho/O1.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
@@ -0,0 +1,2 @@
+d n theta epsilon -log(L)
+0 1178056169 6.99e-04<7.01e-04<7.03e-04 1.41e-04<1.42e-04<1.42e-04 1.63e+09
diff --git a/quarto-to-wiki/quarto-example-verena/mlRho/O11.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt b/quarto-to-wiki/quarto-example-verena/mlRho/O11.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
new file mode 100644
index 0000000..12b46cd
--- /dev/null
+++ b/quarto-to-wiki/quarto-example-verena/mlRho/O11.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
@@ -0,0 +1,2 @@
+d n theta epsilon -log(L)
+0 1177834015 5.92e-04<5.94e-04<5.95e-04 1.21e-04<1.21e-04<1.21e-04 1.62e+09
diff --git a/quarto-to-wiki/quarto-example-verena/mlRho/O15.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt b/quarto-to-wiki/quarto-example-verena/mlRho/O15.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
new file mode 100644
index 0000000..5a603c0
--- /dev/null
+++ b/quarto-to-wiki/quarto-example-verena/mlRho/O15.merged.rmdup.merged.realn.mapped_q30.subs_dp6.5.noCpG_ref.repma.autos.mlRho.txt
@@ -0,0 +1,2 @@
+d n theta epsilon -log(L)
+0 1188951750 7.35e-04<7.37e-04<7.39e-04 1.24e-04<1.24e-04<1.24e-04 1.64e+09
diff --git a/quarto-to-wiki/quarto-example-verena/mlRho/O16.merged.rmdup.merged.realn.noCpG_ref.repma.autos.mlRho.txt b/quarto-to-wiki/quarto-example-verena/mlRho/O16.merged.rmdup.merged.realn.noCpG_ref.repma.autos.mlRho.txt
new file mode 100644
index 0000000..b5b7808
--- /dev/null
+++ b/quarto-to-wiki/quarto-example-verena/mlRho/O16.merged.rmdup.merged.realn.noCpG_ref.repma.autos.mlRho.txt
@@ -0,0 +1,2 @@
+d n theta epsilon -log(L)
+0 1071917495 6.86e-04<6.88e-04<6.89e-04 1.45e-04<1.45e-04<1.45e-04 1.48e+09
diff --git a/quarto-to-wiki/quarto-example-verena/quarto-example-verena.html b/quarto-to-wiki/quarto-example-verena/quarto-example-verena.html
new file mode 100644
index 0000000..24a5a39
--- /dev/null
+++ b/quarto-to-wiki/quarto-example-verena/quarto-example-verena.html
@@ -0,0 +1,3873 @@
+
+
+
+
+
+
+
+
+
+
+
+
+