Analysis ReportsThe BWA Whole Genome Sequencing app provides an overview of statistics per sample on the sample pages. A brief description of the metrics is below. Alignment Summary
Small Variants Summary This table provides metrics about the number of SNVs, insertions, and deletions.
Variants by Sequence Context
Variants by Consequence
Structural Variants Summary This table breaks structural variant output into the classes of variants called, and reports the total number and their overlap with annotated genes. All counts are based on PASS filter variants.
Coverage Histogram The coverage histogram shows the number of reference bases plotted against the depth of coverage (read depth). It has the following features:
Figure 4 BWA Whole Genome Sequencing Coverage Histogram
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