Coverage and Depth
EXPERIMENTAL FEATURE
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Data Types
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SAM, BAM and FASTQ
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Usage
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genocat --show-coverage my-file.bam.genozip
genocat --show-coverage=all my-file.bam.genozip
genocat --show-coverage=one *.bam.genozip
genocat --show-coverage my-file.fq.genozip
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Description
Displays the per-chromosome reads, bases, % of total bases that are on this chromosome and Depth. With the argument =all, shows all contigs, not just primary chromosomes. With the argument =one, shows just a one number summary of coverage (the same number that appears as the Depth on the All contigs line).
Output
Output is space-separated if sent to a terminal, and tab-separated if redirected to a file or pipe.
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$ genocat.exe --coverage my-sample.bam.genozip
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--coverage for: my-sample.bam.genozip
Contig LN Reads Bases Bases Depth
1 249.3 Mb 61,215,549 9.0 Gb 7.1 % 36.10
2 243.2 Mb 63,342,488 9.3 Gb 7.3 % 38.26
3 198.0 Mb 50,819,357 7.5 Gb 5.9 % 37.76
4 191.2 Mb 48,131,726 7.1 Gb 5.6 % 37.04
5 180.9 Mb 46,495,225 6.8 Gb 5.4 % 37.81
6 171.1 Mb 43,659,445 6.4 Gb 5.0 % 37.53
7 159.1 Mb 41,171,496 6.0 Gb 4.7 % 38.01
8 146.4 Mb 38,081,676 5.6 Gb 4.4 % 38.27
9 141.2 Mb 31,755,198 4.7 Gb 3.7 % 33.05
10 135.5 Mb 34,954,121 5.1 Gb 4.0 % 37.90
11 135.0 Mb 35,234,129 5.2 Gb 4.1 % 38.38
12 133.9 Mb 34,523,219 5.1 Gb 4.0 % 37.91
13 115.2 Mb 24,526,664 3.6 Gb 2.8 % 31.32
14 107.3 Mb 23,525,557 3.5 Gb 2.7 % 32.21
15 102.5 Mb 22,613,925 3.3 Gb 2.6 % 32.41
16 90.4 Mb 23,675,707 3.5 Gb 2.7 % 38.41
17 81.2 Mb 22,148,439 3.2 Gb 2.5 % 40.01
18 78.1 Mb 19,542,517 2.9 Gb 2.3 % 36.81
19 59.1 Mb 16,374,766 2.4 Gb 1.9 % 40.50
20 63.0 Mb 16,530,922 2.4 Gb 1.9 % 38.52
21 48.1 Mb 9,811,790 1.4 Gb 1.1 % 29.93
22 51.3 Mb 10,238,901 1.5 Gb 1.2 % 29.26
X 155.3 Mb 20,421,365 3.0 Gb 2.3 % 19.29
Y 59.4 Mb 3,971,007 582.0 Mb 0.5 % 9.80
MT 16.6 Kb 105,906 15.5 Mb 0.0 % 937.41
Other contigs 28,989,258 4.1 Gb 3.2 %
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All contigs 771,860,353 113.3 Gb 88.8% 36.60
Soft clip 1.2 Gb 0.9 %
Unmapped 17,071,958 2.4 Gb 1.9 %
Supplementary 1,028,655 52.2 Mb 0.0 %
Duplicate 71,068,615 10.6 Gb 8.3 %
TOTAL 861,029,581 127.5 Gb 100.0%
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Details
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Length is defined in the header of the SAM/BAM, or in the reference file used to compress it, or in the case of a header-less SAM file that was compressed without a reference - the highest coordinate of the contig that appears in the file.
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Contig includes all contigs present in the file if run with --coverage=all, or if not, just contigs with a name of up to 5 characters, and all other contigs are summed up in the other contings line. The All contigs line sums up the values for all contigs present in the file.
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Unmapped, Failed filters, Duplicate, Secondary, Supplementary (together: Excluded alignments) are SAM alignments with the appropriate SAM FLAG set (i.e. 0x4, 0x200, 0x400, 0x100, 0x800 respectively). Alignments missing an RNAME are also counted as unmapped irrespective of their FLAG. Alignments can count in only one category even if multiple flags are set, with this order of precedence.
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Soft clip are bases with an S (Soft Clip) CIGAR (see 1.4.6 here), but not counting those on Excluded alignments.
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The Reads and Bases reported for each Contig exclude Excluded alignments and the Bases also exclude Soft clip bases.
Depth is Bases divided by the Length (LN) of the contig.
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Using with FASTQ
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This works both on SAM/BAM and on FASTQ. For FASTQ, the mapping to contigs is as reported by the Genozip Aligner. The Genozip Aligner maps reads for compression purposes and does not attempt to map them according to the biological truth. However, usually the large majority of reads are in fact mapped to their correct position, so this can give a reasonable approximation of coverage of the data directly from FASTQ without needing to map it to BAM.
Questions? support@genozip.com