# CoverageAlleles

Auto-generated from the config schema in the source — see the [config guide](https://jbrowse.org/jb2/docs/config_guide) for concepts. Built into JBrowse core. [View source](https://github.com/GMOD/jbrowse-components/blob/main/packages/alignments-core/src/coverageAllelesConfigSchema.ts).

The coverage band's `alleles` layer: the colored segment each mismatched
base takes in its position's depth bar. Its `filter` keeps the segments
whose `fraction`, the allele's share of the position's depth, passes;
the grey depth bar shows through where a segment is left out, and
everywhere under `show: false`. The modification bars are not allele
segments: `pileup.bases` draws them, and nothing here hides or floors
them.

## Example usage

```js
{
  type: 'LinearAlignmentsDisplay',
  coverage: { alleles: { filter: [{ field: 'fraction', gte: 0.2 }] } },
}
```

```js
{ type: 'LinearAlignmentsDisplay', coverage: { alleles: { show: false } } }
```

## Config slots

A setting written to it names members one by one: a member left out stays as it is, and `null` resets one. Slot types (`fileLocation`, `frozen`, ...) are explained in the [config slot types reference](https://jbrowse.org/jb2/docs/config_guides/slot_types). Slots a base configuration contributes are listed here too, so this table is the whole surface.

| Slot | Description |
| --- | --- |
| **show**<br>[`boolean`](https://jbrowse.org/jb2/docs/config_guides/slot_types#boolean) = <code>true</code> | color the allele segments of the depth bars; off, the bars are plain grey |
| **filter**<br>[FieldPredicate](../fieldpredicate) | Entries on `fraction`, a floor from 0 to 1 written `gte`, the one test the band's draw makes. Empty colors every mismatch, sequencing errors included. Distinct from `pileup.fadeLowFrequency`, which fades the pileup's marks by the same share through a depth-dependent threshold. |