How to use (3 steps)
- Select an example or enter target size (genome size / total target region).
- Enter read count (PE/SE) or total yield (Gb).
- Average depth appears. Adjust factors or use inverse calculation if needed.
This is an estimate. Real coverage is not uniform and varies with duplicates, GC bias, design, and analysis. Verify with QC coverage distributions.
Inputs
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Target size
WGS uses genome size; Exome/Panel uses total target size (bp).
Examples: 3.2 Gb (human WGS approx) / 50 Mb (human exome approx)
Input mode
Factors (0–1)
You can keep defaults for a rough estimate.
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Options
≥k× is a Poisson-based guide assuming uniform random coverage. Real data varies (at high depth, a normal approximation may be used).
Results (average depth)
Intermediate calculations (raw → usable → mapped → on-target → unique)
| step | bases (auto units) |
|---|
≥k× proportion (guide)
| threshold | P(depth ≥ k) |
|---|
Guide based on Poisson with mean depth λ (not definitive due to non-uniform coverage).
How it’s calculated
- Compute raw_bases from read counts (PE/SE) or total yield (Gb).
- Apply usable, mapping, on-target, and duplicate rates (1-duplicate) to estimate unique on-target bases.
- Average depth = unique_on_target_bases / target_size.
- ≥k× can be shown as a Poisson-based guide.
Average depth is useful, but uniformity is separate. Confirm with coverage distribution QC.
Use this page for rough depth planning before sequencing or QC review
This calculator estimates average depth from reads, read length, or total yield plus quality factors. Open NGS Library Concentration when the bottleneck is molarity or dilution, use A260 Calculator for nucleic-acid concentration and purity, and switch to qPCR ΔΔCt when you are interpreting expression rather than sequencing depth.
- Set target size and input mode first so the depth baseline is meaningful.
- Tune usable, mapping, on-target, and duplicate factors only after the raw-data assumption is clear.
- Treat ≥k× as a planning guide and validate real uniformity with downstream coverage QC.
FAQ
How many reads are needed for 30× WGS?
It depends on target size, read length, and factors (mapping rate, etc.). Use inverse calculation for your conditions.
What is the on-target rate?
A rough fraction of usable reads that land on the target region (varies by kit/conditions).
If the average depth is the same, is every region the same depth?
No. The average is just an average, and real coverage varies. Use this as a guide.
Is the ≥k× proportion accurate?
It is a Poisson-based guide assuming uniform random coverage. Real data varies.
What should I check first before trusting this estimate?
Confirm read length, paired-end mode, mapped-read rate, and target size. Those four values explain most mismatches between this estimate and your planned experiment.
Related tools
- NGS library concentration (ng/µL → nM) | dilution | CalcBEConvert mass concentration to molar concentration before you estimate sequencing depth or pooling ratios.
- qPCR standard curve calculator | efficiency, slope, R² | CalcBECheck amplification efficiency and curve quality when you are validating assay performance around your sequencing workflow.
- ΔΔCt calculator | fold change, replicates, log2 | CalcBEUse a related quantification workflow when you need expression-style interpretation rather than sequencing coverage.
- A260 Calculator (DNA/RNA Concentration & Purity) | CalcBEEstimate nucleic-acid concentration and purity from absorbance before library prep or dilution planning.
Comments
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