Coverage Metrics Report
The coverage metrics report outputs a _coverage_metrics.csv file, which provides metrics over a region, where the region can be the genome, a target region, or a QC coverage region. The first column of the output file contains the section name COVERAGE SUMMARY and the second column is empty for all metrics.
The following criteria are used when calculating coverage:
| • | Duplicate reads and clipped bases are ignored. |
| • | Only reads with MAPQ > min MAPQ and bases with BQ > min BQ are considered. |
The following table lists the calculated metrics:
|
Metric |
Description |
|---|---|
|
Aligned bases in region |
Number of uniquely mapped bases to region and the percentage relative to the number of uniquely mapped bases to the genome. |
|
Average alignment coverage over region |
Number of uniquely mapped bases to region divided by the number of sites in region. |
|
Uniformity of coverage (PCT > 0.2*mean) over region |
Percentage of sites with coverage greater than 20% of the mean coverage in region. |
|
PCT of region with coverage [ix, inf) |
Percentage of sites in region with at least ix coverage, where i can equal 100, 50, 20, 15, 10, 3, 1 and 0. |
|
PCT of region with coverage [ix, jx) |
Percentage of sites in region with at least ix but less than jx coverage, where (i, j) can equal (50, 100), (20, 50), (15, 20), (10, 15), (3, 10), (1, 3) and (0, 1). |
|
Average chromosome X coverage over region |
Total number of bases that aligned to the intersection of chromosome X with region divided by the total number of loci in the intersection of chromosome X with region. If there is no chromosome X in the reference genome or the region does not intersect chromosome X, this metric shows as NA. |
|
Average chromosome Y coverage over region |
Total number of bases that aligned to the intersection of chromosome Y with region divided by the total number of loci in the intersection of chromosome Y with region. If there is no chromosome Y in the reference genome or the region does not intersect chromosome Y, this metric shows as NA. |
|
XAvgCov/YAvgCov ratio over genome/target region |
Average chromosome X alignment coverage in region divided by the average chromosome Y alignment coverage in region. If there is no chromosome X or chromosome Y in the reference genome or the region does not intersect chromosome X or Y, this metric shows as NA. |
|
Average mitochondrial coverage over region |
Total number of bases that aligned to the intersection of the mitochondrial chromosome with region divided by the total number of loci in the intersection of the mitochondrial chromosome with region. If there is no mitochondrial chromosome in the reference genome or the region does not intersect mitochondrial chromosome, this metric shows as NA. |
|
Average autosomal coverage over region |
Total number of bases that aligned to the autosomal loci in region divided by the total number of loci in the autosomal loci in region. If there is no autosome in the reference genome, or the region does not intersect autosomes, this metric shows as NA. |
|
Median autosomal coverage over region— |
Median alignment coverage over the autosomal loci in region. If there is no autosome in the reference genome or the region does not intersect autosomes, this metric shows as NA. |
|
Mean/Median autosomal coverage ratio over region |
Mean autosomal coverage in region divided by the median autosomal coverage in region. If there is no autosome in the reference genome or the region does not intersect autosomes, this metric shows as NA. |
|
Aligned reads in region— |
Number of uniquely mapped reads to region and percentage relative to the number of uniquely mapped reads to the genome. When region is the target BED, this metric is equivalent to and replaces Capture Specificity based on target region. |
The following is an example of the contents of the _coverage_metrics.csv file:
COVERAGE SUMMARY,,Aligned bases,148169295474
COVERAGE SUMMARY,,Aligned bases in genome,148169295474,100.00
COVERAGE SUMMARY,,Average alignment coverage over genome,46.08
COVERAGE SUMMARY,,Uniformity of coverage (PCT > 0.2*mean) over genome,91.01
COVERAGE SUMMARY,,PCT of genome with coverage [100x: inf),0.25
COVERAGE SUMMARY,,PCT of genome with coverage [ 50x: inf),50.01
COVERAGE SUMMARY,,PCT of genome with coverage [ 20x: inf),89.46
COVERAGE SUMMARY,,PCT of genome with coverage [ 15x: inf),90.51
COVERAGE SUMMARY,,PCT of genome with coverage [ 10x: inf),91.01
COVERAGE SUMMARY,,PCT of genome with coverage [ 3x: inf),91.69
COVERAGE SUMMARY,,PCT of genome with coverage [ 1x: inf),92.10
COVERAGE SUMMARY,,PCT of genome with coverage [ 0x: inf),100.00
COVERAGE SUMMARY,,PCT of genome with coverage [ 50x:100x),49.76
COVERAGE SUMMARY,,PCT of genome with coverage [ 20x: 50x),39.45
COVERAGE SUMMARY,,PCT of genome with coverage [ 15x: 20x),1.04
COVERAGE SUMMARY,,PCT of genome with coverage [ 10x: 15x),0.51
COVERAGE SUMMARY,,PCT of genome with coverage [ 3x: 10x),0.67
COVERAGE SUMMARY,,PCT of genome with coverage [ 1x: 3x),0.42
COVERAGE SUMMARY,,PCT of genome with coverage [ 0x: 1x),7.90
COVERAGE SUMMARY,,Average chr X coverage over genome,24.70
COVERAGE SUMMARY,,Average chr Y coverage over genome,20.96
COVERAGE SUMMARY,,Average mitochondrial coverage over genome,20682.19
COVERAGE SUMMARY,,Average autosomal coverage over genome,47.81
COVERAGE SUMMARY,,Median autosomal coverage over genome,48.62
COVERAGE SUMMARY,,Mean/Median autosomal coverage ratio over genome,0.98
COVERAGE SUMMARY,,XAvgCov/YAvgCov ratio over genome,1.18
COVERAGE SUMMARY,,XAvgCov/AutosomalAvgCov ratio over genome,0.52
COVERAGE SUMMARY,,YAvgCov/AutosomalAvgCov ratio over genome,0.44
COVERAGE SUMMARY,,Aligned reads,1477121058
COVERAGE SUMMARY,,Aligned reads in genome,1477121058,100.00