Table 1 Epitope homology results for four genomes. M. tuberculosis var. bovis strains AF2122/97 (virulent, reference), BCG-1 Russia (attenuated, reference), 10-7428 (virulent, newly sequenced), and Ravenel (attenuated, newly sequenced). Epitopes (n = 4894) were selected from IEDB.org and filtered to 4818 to query against the 4 genomic .fna files indexed for tblastn. The raw hits row indicates the number of epitopes aligning anywhere in the genome designated per column. Matches indicates 100% similarity to at least one epitope variant in the IEDB dataset. Mismatches indicates alignment but with #aa differences (indicated per column, 1, 2, or 3 mismatches). Finally, Unique Mismatches indicates the mismatched sequence does not also map perfectly to any other variant epitope sequences from IEDB or, with the exception of blue-shaded AF2122/97 cells, that these changes are not observed in AF2122/97 epitopes either. Sequences with gaps or with more than 3 mismatches are not included in the analysis, so values do not sum to the original Raw Hits value. *AF2122/97 values are not subtracted from what may be MBO wild-type variation like other strains are, and thus its values should not be compared directly.
