Full Res Report

The Full Res Report outputs a _full_res.bed file. This file is tab-delimited file and has as its first three columns the standard BED fields, and as its fourth column the depth. Each record in the file is for a given interval that has a constant depth. If the depth changes, then a new record is written to the file. Alignments that have a mapping quality value of 0, duplicate reads, and clipped bases are not counted towards the depth.

Only base positions that fall under the user-specified coverage-region bed regions are present in the _full_res.bed output file.

The _full_res.bed file structure is similar to the output file of bedtools genomecov -bg. The contents are identical if the bedtools command line is executed after filtering out alignments with mapping quality value of 0, and possibly filtering by a target BED (if specified).

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

chr1 121483984 121483985 10

chr1 121483985 121483986 9

chr1 121483986 121483989 8

chr1 121483989 121483991 7

chr1 121483991 121483992 6

chr1 121483992 121483993 4

chr1 121483993 121483994 2

chr1 121483994 121484039 1

chr1 121484039 121484043 2

chr1 121484043 121484048 3

chr1 121484048 121484050 7

chr1 121484050 121484051 11

chr1 121484051 121484052 17

chr1 121484052 121484053 149

chr1 121484053 121484054 323

chr1 121484054 121484055 2414