Figure 5.

Only MiST detected the variant in gene NLRC3, R282W (chr16:3614094 on hg19), which was confirmed by Sanger sequencing. (a) Alignment View and (b) Pileup View. In the pileup view, column 1 is the position relative to the start of the genomic fragment, column 2 is the reference allele, column 3 gives coverage at that position, with the number of reads in forward and reverse directions (±) shown within parenthesis, column 4 gives the coverage for the mutated allele and the non-reference allele in the reads are shown in column 5. The name of the file contains the position of the fragment in the genome. MiST calls this SNP despite a strong skew (strand-bias) in the mutant allele because the reference allele also shows a strong skew.