Figure 4
From: From next-generation resequencing reads to a high-quality variant data set
Indicators of false positive variant calls. Examples: (a) Variants in a region with exceptionally high coverage that might result from an incomplete reference sequence, unresolved collapsed copy number variations or repeats. Coverage is shown as vertical bars in the top panel. Alignments are provided in the lower panel with reads indicated as gray horizontal bars, variants as colored ticks, insertions as purple Is and deletions as black horizontal lines. (b) Variants only supported by low-quality reads (reads with a mapping quality of <5 are shown in red). (c) Variant supported by reads that show a strand bias (that is, the variant is stronger supported by the forward strand (red) than the reverse strand (blue)). (d) Region with a high clustering of variants. All examples were plotted using IGV (Robinson et al., 2011).
