Poisson Uncovered Fraction
Estimate uncovered genome fraction under the uniform independent Poisson coverage model.
Description
Under independent uniform random coverage, a base’s depth follows a Poisson model.
Under independent uniform random coverage, a base’s depth follows a Poisson model. The zero-depth probability falls exponentially as mean depth increases.1
Estimate uncovered genome fraction under the uniform independent Poisson coverage model.
When to use Poisson Uncovered Fraction
Use this for the following task: Estimate uncovered genome fraction under the uniform independent Poisson coverage model.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Poisson Uncovered Fraction and understand its results
- Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
- Enter foldCoverage, genomeBases using the field table, then run the tool.
- Read uncoveredFraction, expectedUncoveredBases. Interpret flags, units, ordering and placeholder values using the rules below.
- Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.
| Input field | Meaning | Value type and bounds | Requirement |
|---|---|---|---|
| foldCoverage | Fold coverage | number; minimum 0 | Required |
| genomeBases | Genome bases | integer; minimum 1 | Required |
Supply nonnegative coverage and positive genome length. Use a scaled exponent calculation when the probability becomes subnormal to retain a representable expected count.2
uncoveredFraction = exp(−foldCoverage); expectedBases = genomeBases exp(−foldCoverage) This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| uncoveredFraction | Uncovered fraction | number |
| expectedUncoveredBases | Expected uncovered bases | number |
{
"input": {
"foldCoverage": 1,
"genomeBases": 1000
},
"output": {
"uncoveredFraction": 0.36787944117144233,
"expectedUncoveredBases": 367.87944117144235
}
}Limitations and assumptions
Real coverage can be biased and correlated. The result is an expectation, not a guarantee of complete sequencing.
The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.
Alternative or Complementary methods
Choose Sequencing Fold Depth for this operation: Compute theoretical sequencing depth from individual read count, read length, and genome size. For a complementary task, use Callable Depth Fraction for this operation: Calculate callable-base percentage from a depth histogram and minimum calling depth.
Further background: Background specification: Poisson Uncovered Fraction.
References
Similar or alternative tools
- Sequencing Fold Depth
Compute theoretical sequencing depth from individual read count, read length, and genome size.
- Callable Depth Fraction
Calculate callable-base percentage from a depth histogram and minimum calling depth.