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Update orgStat.md
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add some missing underscore
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@ggautreau
ggautreau authored Nov 24, 2023
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Showing 1 changed file with 27 additions and 27 deletions.
54 changes: 27 additions & 27 deletions docs/user/Flat/orgStat.md
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Expand Up @@ -6,37 +6,37 @@ This file comprises 32 columns described in the following table:

| Column | Description |
|-----------------------------|-----------------------------------------------------------------------------------------------|
| Organism name | Name of the organism to which the provided genome belongs |
| Contigs | Number of contigs present in the genome |
| Genes | Total number of genes in the genome |
| Fragmented genes | Number of genes flagged as fragmented. Refer to the [defragmentation](../step-by-step/clustering.md#defragmentation) section for detailed information on the fragmentation process. |
| Families | Total number of gene families present in the genome |
| Families_with_fragments | Number of families containing fragmented genes |
| Families_in_multicopy | Number of families present in multiple copies |
| Soft_core_families | Number of families categorized as soft core |
| Soft_core_genes | Number of genes within soft core families |
| Exact_core_families | Number of families categorized as exact core |
| Exact_core_genes | Number of genes within exact core families |
| Persistent_genes | Number of genes classified as persistent |
| Persistent_fragmented genes | Number of genes flagged as persistent and fragmented |
| Persistent_families | Number of families categorized as persistent |
| Organism_name | Name of the organism to which the provided genome belongs |
| Contigs | Number of contigs present in the genome |
| Genes | Total number of genes in the genome |
| Fragmented_genes | Number of genes flagged as fragmented. Refer to the [defragmentation](../step-by-step/clustering.md#defragmentation) section for detailed information on the fragmentation process. |
| Families | Total number of gene families present in the genome |
| Families_with_fragments | Number of families containing fragmented genes |
| Families_in_multicopy | Number of families present in multiple copies |
| Soft_core_families | Number of families categorized as soft core |
| Soft_core_genes | Number of genes within soft core families |
| Exact_core_families | Number of families categorized as exact core |
| Exact_core_genes | Number of genes within exact core families |
| Persistent_genes | Number of genes classified as persistent |
| Persistent_fragmented_genes | Number of genes flagged as persistent and fragmented |
| Persistent_families | Number of families categorized as persistent |
| Persistent_families_with_fragments | Number of persistent families containing fragmented genes |
| Persistent_families_in_multicopy | Number of persistent families present in multiple copies |
| Shell_genes | Number of genes classified as shell |
| Shell_fragmented_genes | Number of genes flagged as shell and fragmented |
| Shell_families | Number of families categorized as shell |
| Shell_families_with_fragments | Number of shell families containing fragmented genes |
| Shell_families_in_multicopy | Number of shell families present in multiple copies |
| Cloud_genes | Number of genes classified as cloud |
| Cloud_fragmented_genes | Number of genes flagged as cloud and fragmented |
| Cloud_families | Number of families categorized as cloud |
| Cloud_families_with_fragments | Number of cloud families containing fragmented genes |
| Cloud_families_in_multicopy | Number of cloud families present in multiple copies |
| Persistent_families_in_multicopy | Number of persistent families present in multiple copies |
| Shell_genes | Number of genes classified as shell |
| Shell_fragmented_genes | Number of genes flagged as shell and fragmented |
| Shell_families | Number of families categorized as shell |
| Shell_families_with_fragments | Number of shell families containing fragmented genes |
| Shell_families_in_multicopy | Number of shell families present in multiple copies |
| Cloud_genes | Number of genes classified as cloud |
| Cloud_fragmented_genes | Number of genes flagged as cloud and fragmented |
| Cloud_families | Number of families categorized as cloud |
| Cloud_families_with_fragments | Number of cloud families containing fragmented genes |
| Cloud_families_in_multicopy | Number of cloud families present in multiple copies |
| Completeness | Proportion of persistent families present in the genome; expected to be close to 100 for isolates |
| Contamination | Proportion of single copy persistent families found in multiple copy in the genome. |
| Fragmentation | Proportion of families with fragmented genes in the genome |
| RGPs | Number of Regions of Genomic Plasticity identified |
| Spots | Number of spot IDs in which the RGPs are inserted |
| RGPs | Number of Regions of Genomic Plasticity identified |
| Spots | Number of spot IDs in which the RGPs are inserted |
| Modules | Number of module IDs within gene families |


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