Per Contig Mean Coverage Report
The Contig Mean Coverage report generates a _contig_mean_cov.csv file, which contains the estimated coverage for all contigs, and an autosomal estimated coverage. The file includes the following three columns:
|
Column 1 |
Column 2 |
Column 3 |
|---|---|---|
|
Contig name |
Number of bases aligned to that contig, which excludes bases from duplicate marked reads, reads with MAPQ=0, and clipped bases. |
The estimated covered, calculated as follows. Number of bases aligned to the contig (ie, Col2) divided by length of the contig or (if a target bed is used) the total length of the target region spanning that contig. |