Details of B. anthracis polymorphisms not detected by the SOLiD™ system. Sequence alignments of B. anthracis Sterne (top line) versus Ames ancestor (bottom line). Red line indicates coverage depth of uniquely mapping A2012 SOLiD™ system reads at each position. Sterne chromosomal coordinates are given below the alignment. (Top) A region of high SNP density (13 SNPs in 40 bp) and small indels in GBAA_2450. (Bottom) In GBAA_1572, SNPs occur in a region containing a 27 bp repeat (alternating blue and orange blocks, with repeat number below). Relative to Ames ancestor, the Sterne genome lacks two repeat units. The four SNPs are adjacent to the indel breakpoint. Low unique coverage to the left of the SNPs is due to three perfect repeats (numbers 4, 5 and 6). Bases that differ from the consensus sequence are underlined.