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.
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.
Related tools
- DNA/RNA concentration ↔ mol ↔ copy number
For library prep and input conversion.
- qPCR standard curve calculator
Similar quantification workflow (standards → curve → inverse).
Comments
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