Additional file 2 of Whole-exome sequencing of BRCA-negative breast cancer patients and case–control analyses identify variants associated with breast cancer susceptibility

Additional file 2: Fig. S2. Representative IGV screenshots of unambiguous versus ambiguous alignments. A A heterozygous SNV with equal support for both reference and alternate bases; B deletion, as indicated by clear gaps in the read alignment; and C insertion, as represented by a thin vertical line flanked by mapped bases on both sides. Red boxes indicate where the variants are expected to appear. In comparison, the heterozygous nonsynonymous SNVs D MUC4 NM_018406.7:c.G8461A E KMT2C NM_170606.3:c.C2689T F KMT2C NM_170606.3:c.C2710T and G HLA-DRB1 NM_002124.3:c.C301T have fewer reads supporting the alternate base; the frameshift deletions H HLA-A NM_001242758.1:c.268delA and I HLA-DRB1 NM_002124.3:c.118_122del are not associated with any obvious gaps in read alignments; nor is the frameshift insertion J HLA-DRB1 NM_002124.3:c.126_127insTTAAGTTT represented by insertions in its read alignments.