Coverage Report

The cov_report report generates a full-coverage-report file in both BED and CSV formats. The first three columns are standard BED fields. The remaining column fields are statistics calculated over the interval region specified on the same record line.

The following table lists the appended columns.

Column	Description
total_cvg	The total coverage value.
mean_cvg	The mean coverage value.
Q1_cv	The lower quartile (25th percentile) coverage value.
median_cvg	The median coverage value.
Q3_cvg	The upper quartile (75th percentile) coverage value.
min_cvg	The minimum coverage value.
max_cvg	The maximum coverage value.
pct_above_X	Indicates the percentage of bases over the specified interval region that had a depth coverage greater than X.

The following is an example of the contents of the _cov_report.bed file:

chrom  start      end        total_cvg  mean_cvg  Q1_cvg  median_cvg  Q3_cvg  min_cvg  max_cvg  pct_above_5 …
chr5   34190121   34191570   76636      52.89     44.00   54.00       60.00   32       76       100.00      …
chr5   34191751   34192380   39994      63.58     57.00   61.00       69.00   50       85       100.00      …
chr5   34192440   34192642   10074      49.87     47.00   49.00       51.00   44       62       100.00      …
chr9   66456991   66457682   31926      46.20     39.00   45.00       52.00   27       65       100.00      …
chr9   68426500   68426601   4870       48.22     42.00   48.00       54.00   39       58       100.00      …
chr17  41465818   41466180   24470      67.60     4.00    66.00       124.00  2        153      66.30       …
chr20  29652081   29652203   5738       47.03     40.00   49.00       52.00   34       58       100.00      …
chr21  9826182    9826283    4160       41.19     23.00   52.00       58.00   5        60       99.01       …