Table 2 Summary of M. tuberculosis data sets used for joint genotyping. “Genome inside sites” is the total length of all reference alleles across all sites after clustering. It is reported as the total number of base pairs, and in parentheses as a percentage of the 4.4Mbp H37Rv reference genome. SNP sites is the number of sites where all alleles have length 1
From: Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes
Data set | Number of samples | Unique variants | Excluded variants | Sites after clustering | Genome inside sites (bp(%)) | Total alleles | SNP sites |
|---|---|---|---|---|---|---|---|
Walker 2013 | 385 | 31,548 | 231 | 30,621 | 41,437 (1%) | 62,690 | 27,639 |
Mykrobe | 13,411 | 699,484 | 6,259 | 593,584 | 756,003 (17%) | 1,414,723 | 552,543 |
CRyPTIC | 15,215 | 718,863 | 6,576 | 611,269 | 778,949 (18%) | 1,469,100 | 568,224 |