Allele frequency distribution with local re-alignment of U87MG. SRMA was applied to the alignments produced with BFAST of a human cancer cell line (U87MG; SRA009912.1). Variants were called with SAMtools before and after application of SRMA (see Materials and methods). Homozygous and heterozygous calls were examined independently using zygosity calls produced by SAMtools. The observed non-reference allele frequency for SNPs, deletions, and insertions are plotted for homozygous (left panels) or heterozygous variants (right panels). Ideally, non-reference allele frequencies for homozygous and heterozygous variants approach 1.0 and 0.5, respectively. The absolute counts of observed variants are plotted (y-axis) against non-reference allele frequency ranges (x-axis).
Homer and Nelson Genome Biology 2010 11:R99 doi:10.1186/gb-2010-11-10-r99