codoncounts.zip

This directory contains codon counts analysed by genomegaMap in D. J. Wilson and The CRyPTIC Consortium (2019). The codon counts for a particular coding sequence in the Mycobacterium tuberculosis H37Rv reference genome (version 2, genbank accession number NC_000962.2) are contained in each codoncounts.txt file, where the filename is prefixed by the gene identifier. Each file contains a matrix of integers with no row or column names, where element (row i, column j) of the matrix records the number of genomes exhibiting triplet j at codon position i. Positions are ordered as per NC_000962.2, beginning with the start codon. Terminal stop codons are not included. Triplets are ordered as follows:TTT,TTC,TTA,TTG,TCT,TCC,TCA,TCG,TAT,TAC,TGT,TGC,TGG,CTT,CTC,CTA,CTG,CCT,CCC,CCA,CCG,CAT,CAC,CAA,CAG,CGT,CGC,CGA,CGG,ATT,ATC,ATA,ATG,ACT,ACC,ACA,ACG,AAT,AAC,AAA,AAG,AGT,AGC,AGA,AGG,GTT,GTC,GTA,GTG,GCT,GCC,GCA,GCG,GAT,GAC,GAA,GAG,GGT,GGC,GGA,GGG,---where --- represents any call other than the 61 non-stop codons, including deletions, ambiguous or filtered calls, and premature stop codons. 10,209 genomes were mapped against the H37Rv reference, with details and short read archive accession numbers described in the original paper by The CRyPTIC Consortium and the 100,000 Genomes Project (2018).<br>