mtbDrugResistance

Signatures of selection at drug resistance loci in Mycobacterium tuberculosis

Rmarkdown

drugResistancePopGenSummary.Rmd

Rmarkdown file with code to process and plot upstream analyses

drugResistancePopGenSummary.html

HTML file produced from Rmarkdown

data

160129_Mtb_removeRegions_mergedCloserThan1000bp.bed

Repetitive regions masked from all alignments

bydrug_stats.txt

Diversity statistics for alignments of susceptible and resistant subpopulations of first and second line drugs

drugSpecificStats_lineage2.txt

Diversity statistics for alignments of susceptible and resistant subpopulations in L2

drugSpecificStats_lineage4.txt

Diversity statistics for alignments of susceptible and resistant subpopulations in L4

drugSusceptibilityTotals.txt

Drug susceptibility from phenotypic data

fst_cutoffs.txt

Maximum Fst values when susceptibility is randomly assigned

functionalCategories.TXT

Functional categories previously used in O'Neill et al. 2015 for functional enrichment tests

gappedPositions_5percThreshold.txt

Positions where > 5% of isolates have a gap or missing data character

geneLengths.txt

Gene lengths from H37Rv annotation

genewise_pi.txt

Pi values for each gene in resistant and susceptible subpopulations

genewise_theta.txt

Theta values for each gene in resistant and susceptible subpopulations

genewiseStats.txt

Diversity statistics for each gene using entire sample

genewiseStats_lineage2.txt

Diversity statistics for each gene in L2

genewiseStats_lineage4.txt

Diversity statistics for each gene in L4

homoplastic_indels.txt

List of indels identified as homoplastic

homoplastic_merged_indels.txt

List of indels indentified as homoplastic when indels from the same gene are considered identical

homoplastic_snps_counts.txt

List of homoplastic SNPs and the number of times they occcur on the phylogeny

indel_descriptions.txt

Indel names, types, and impacted genes

lineage2_genewise_pi.txt

Pi values for each gene in resistant and susceptible subpopulations in L2

lineage2_genewise_theta.txt

Theta values for each gene in resistant and susceptible subpopulations in L2

lineage2_wcFst_mergedIndels.txt

Fst values for indels in L2

lineage4_genewise_pi.txt

Pi values for each gene in resistant and susceptible subpopulations in L4

lineage4_genewise_theta.txt

Theta values for each gene in resistant and susceptible subpopulations in L4

lineage4_wcFst_mergedIndels.txt

Fst values for indels in L4

merged_indels_description.txt

Genes and types of indels after merging

mtb_drugResistance_snps.txt

Location, type, and gene of all SNPs in alignments

resistanceGeneNames.txt

List of resistance loci

rv_numbers.txt

Rv numbers for genes in H37Rv genome

tree.newick

Phylogenetic tree estimated with FastTree

wcFst.txt

Fst values for SNPs

wcFst_indels.txt

Fst values for indels

wcFst_indels_lineage2.txt

Fst values for indels in L2

wcFst_indels_lineage4.txt

Fst values for indels in L4

wcFst_lineage2.txt

Fst values for SNPs in L2

wcFst_lineage4.txt

Fst values for SNPs in L4

wcFst_mergedIndels.txt

Fst values of indels when indels from the same gene are considered identical

wholeAlignmentDiversity.txt

Diversity values for entire alignment

scripts

combineIndels.py

Merges indels in the same gene

randomizeFst.py

Calculates Fst after randomly assigning populations

runFst.py

Calculates Fst

selectionStats.py

Calculates diversity statistics for alignments

tables

accessions.txt

Accession numbers and lineage designation for sequence data used (Supplementary Table 1)

drGenesStats.txt

Signatures of selection in known drug resistance genes (Table 2)

fst_homoplasy_table.txt

Homoplastic Fst outliers (Table 3)

tbdream_DB

tbdreamDB.csv

Edited CSV of TB Drug Resistance Database that can be parsed in R (orginally obtained from https://tbdreamdb.ki.se/Info/)