Sequencing Coverage Calculator
Sequencing coverage (read depth) is the average number of times each base in a genome is sequenced. It is calculated using the Lander-Waterman equation: coverage = (read length x number of reads) / genome size. This calculator accepts genome size in megabases (Mb) or basepairs (bp), read length in bp, and total number of reads. It outputs mean coverage in fold (x) and the total bases sequenced. For paired-end sequencing, enter total reads (both pairs counted), not read pairs.
Coverage formula (Lander-Waterman)
Coverage (x) = (read length x number of reads) / genome size (bp)
Total bases = read length x number of reads
This assumes uniform random coverage (shotgun model). In practice, GC-bias and repetitive regions cause non-uniform coverage, so effective coverage is lower than mean coverage.
Common genome sizes and coverage targets
- Human genome: 3,000 Mb (3 Gb). WGS target: 30x for germline, 60x+ for cancer.
- Mouse genome: 2,700 Mb.
- E. coli: 4.6 Mb. 100x coverage needs only 3.07 million 150 bp reads.
- SARS-CoV-2: 29.9 kb. Very deep coverage (10,000x+) needed for minority variant detection.
- Whole exome sequencing: targets approximately 60 Mb; typically 100x coverage.
Frequently asked questions
What is sequencing coverage (read depth)?
Sequencing coverage is the average number of times each base in the genome is represented in the sequencing data. Coverage = (read length x number of reads) / genome size. Higher coverage improves variant detection accuracy and reduces false positives and negatives.
What coverage is needed for whole-genome sequencing?
For human whole-genome sequencing (WGS), 30x is considered minimum for high-quality variant calling; 60-100x is used for cancer genomics or structural variant detection. For targeted capture panels, 200-500x is typical. For RNA-seq, coverage depth is expressed differently (reads per million, RPM).
What is the Lander-Waterman equation?
The Lander-Waterman equation C = NL/G predicts average coverage C from N reads, each of length L bases, over a genome of size G bases. It assumes random read placement (shotgun sequencing). Published by Lander and Waterman in 1988.
How many reads do I need to achieve a target coverage?
Rearranging the equation: N = C x G / L. For 30x coverage of the human genome (3 x 10^9 bp) with 150 bp reads: N = 30 x 3,000,000,000 / 150 = 600,000,000 reads (600 million paired-end reads = 300 million pairs).
What is the difference between mean coverage and uniformity?
Mean coverage is the average depth across all bases (what this calculator computes). Uniformity describes how evenly reads are distributed: a genome could have 30x mean coverage but with some regions at 1x and others at 100x. Uniformity is assessed with breadth of coverage (percentage of bases at or above a minimum depth).
Official sources
- NCBI: Lander ES, Waterman MS. Genomic mapping by fingerprinting, 1988.
- NIH NHGRI: Sequencing the Human Genome.
Reviewed by the CalculatorHub team, edited by James Graham, 15 June 2026. See our methodology.