Fig. 2

Example Classification of Genes Based on Variant Comparisons. Considering the profile of H37Ra-specific variants (those with respect to H37Rv not also appearing in CDC1551), a given gene (blue arrow) is categorized as “supported”, “contradicted”, or “adjusted” by our H37Ra assembly as a result of comparison with the hitherto reference sequence NC_009525.1. The illustration shows examples of the different variant profiles a gene could have and their resulting classifications. Genes in the “supported” and “contradicted” categories are strictly those where our assembly either fully matches the H37Ra reference (supported) or the H37Rv reference (contradicted). Multiple factors may cause a gene to be classified as “adjusted”. Such genes may have variant profiles not fully meeting the criteria of “supported” or “contradicted”, or they may have novel H37Ra-specific variants observed only in our assembly