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samtools-coverage(1) Bioinformatics tools samtools-coverage(1) NAME samtools coverage - produces a histogram or table of coverage per chromo- some SYNOPSIS samtools coverage [options] [in1.sam|in1.bam|in1.cram [in2.sam|in2.bam|in2.cram] [...]] DESCRIPTION Computes the coverage at each position or region and draws an ASCII-art histogram or tabulated text. Coverage is defined as the percentage of positions within each bin with at least one base aligned against it. The tabulated form uses the following headings. rname Reference name / chromosome startpos Start position endpos End position (or sequence length) numreads Number reads aligned to the region (after filtering) covbases Number of covered bases with depth >= 1 coverage Percentage of covered bases [0..100] meandepth Mean depth of coverage meanbaseq Mean baseQ in covered region meanmapq Mean mapQ of selected reads OPTIONS Input options: -b, --bam-list FILE List of input BAM files, one file per line [null] -l, --min-read-len INT Ignore reads shorter than INT base pairs [0] -q, --min-MQ INT Minimum mapping quality for an alignment to be used [0] -Q, --min-BQ INT Minimum base quality for a base to be considered [0] --rf, --incl-flags STR|INT Required flags: skip reads with mask bits unset [null] --ff, --excl-flags STR|INT Filter flags: skip reads with mask bits set [UNMAP,SECONDARY,QC- FAIL,DUP] -d, --depth INT Maximum allowed coverage depth [1000000]. If 0, depth is set to the maximum integer value effectively removing any depth limit. --min-depth INT Minimum coverage depth, below which a position is ignored [1] Output options: -m, --histogram Show histogram instead of tabular output. -D, --plot-depth As above but displays the depth of coverage instead of the percent of coverage. This option can be used to visualize copy number variations in the terminal. -A, --ascii Show only ASCII characters in histogram using colon and fullstop for full and half height characters. -o, --output FILE Write output to FILE [stdout]. -H, --no-header Don't print a header in tabular mode. -w, --n-bins INT Number of bins in histogram. [terminal width - 40] -r, --region REG Show specified region. Format: chr:start-end. -h, --help Shows command help. EXAMPLES Running coverage in tabular mode, on a specific region, with tabs shown as spaces for clarity in this man page. samtools coverage -r chr1:1M-12M input.bam #rname startpos endpos numreads covbases coverage meandepth meanbaseq meanmapq chr1 1000000 12000000 528695 1069995 9.72723 3.50281 34.4 55.8 An example of the histogram output is below, with ASCII block characters replaced by "#" for rendering in this man page. samtools coverage -A -w 32 -r chr1:1M-12M input.bam chr1 (249.25Mbp) > 24.19% | . | Number of reads: 528695 > 21.50% |:: | (132000 filtered) > 18.81% |:: | Covered bases: 1.07Mbp > 16.12% |:: : | Percent covered: 9.727% > 13.44% |:: : . :: : :| Mean coverage: 3.5x > 10.75% |:: :: : :: : : :| Mean baseQ: 34.4 > 8.06% |::::: : :: : : : :| Mean mapQ: 55.8 > 5.37% |::::: :: ::: : ::::: :| > 2.69% |::::: ::: ::: ::: :::::::::| Histo bin width: 343.8Kbp > 0.00% |:::::::::::. :::::::::::::::::::| Histo max bin: 26.873% 1.00M 4.44M 7.87M 12.00M samtools coverage -m -r 'chr1:24500000-25600000' --plot-depth -w 32 -A input.bam chr1 (249.25Mbp) > 38.8 | .::::::: | Number of reads: 283218 > 34.5 | :::::::: | (3327 filtered) > 30.2 | :::::::::. | Covered bases: 1.10Mbp > 25.9 |.:::::.:.::::::::::::::::::::::.| Percent covered: 99.83% > 21.6 |::::::::::::::::::::::::::::::::| Mean coverage: 33.2x > 17.2 |::::::::::::::::::::::::::::::::| Mean baseQ: 37.2 > 12.9 |::::::::::::::::::::::::::::::::| Mean mapQ: 59.3 > 8.6 |::::::::::::::::::::::::::::::::| > 4.3 |::::::::::::::::::::::::::::::::| Histo bin width: 34.5Kbp > 0.0 |::::::::::::::::::::::::::::::::| Histo max cov: 43.117 24.50M 24.84M 25.19M 25.60M AUTHOR Written by Florian P Breitwieser. SEE ALSO samtools(1), samtools-depth(1), Samtools website: <http://www.htslib.org/> samtools-1.23.1 18 March 2026 samtools-coverage(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXAMPLES | AUTHOR | SEE ALSO
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