Supplementary Figure 1: GC%, coverage and informative sites in HLA genes in 8 CLL samples.
From: Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes
(a) A significant negative correlation was observed between GC content and exome coverage (1-way ANOVA, P = 1.6×10−7). Mapping was carried out using BWA with the following parameters: aln task, −q 5 −l 32 −k 2 −o 1; sampe task, −a 300 (b) GC-rich regions of HLA genes have a relative over-abundance of informative (variant) sites (1-way ANOVA, P = 0.0197). (c) Detailed view of GC%, coverage and informative site density in each HLA gene from 1 representative CLL sample. Top row: The x-axis represents the chr6 location. The mid-panel dashed black segments represent exons. GC% (green) decreases in the 5′->3′ direction (HLA-B and HLA-C are located on the negative strand). Coverage (blue) has an opposite trend and increases in the 5′->3′ direction. The informative site density (red) was evaluated as the number of variant sites located in a 50 bp window, and tracked with GC%. Bottom row — the coverage distribution at the variant positions in each of HLA-A, -B and -C.
