# AlignmentsModifications

Auto-generated from the config schema in the source — see the [config guide](https://jbrowse.org/jb2/docs/config_guide) for concepts. Provided by the `alignments` plugin. [View source](https://github.com/GMOD/jbrowse-components/blob/main/plugins/alignments/src/LinearAlignmentsDisplay/alignmentsModificationsConfigSchema.ts).

## Example usage

```js
{
  type: 'LinearAlignmentsDisplay',
  baseColor: 'modifications',
  modifications: { fillUnmarked: true, cytosineContext: 'CHG' },
}
```

```js
{
  type: 'LinearAlignmentsDisplay',
  baseColor: 'modifications',
  modifications: { shownModifications: ['a'], threshold: 50 },
}
```

_See the **Config slots** section below for all available configuration fields._

The alignments displays' `modifications` setting: what the `modifications`
and `bisulfite` fields of [AlignmentsBaseColor](../alignmentsbasecolor)
draw. The by-type view paints each MM/ML call its type's color above
`threshold`; `twoColor` paints the unmodified side blue as well, and
`fillUnmarked` paints every cytosine in `cytosineContext` whether the
basecaller listed it or not, which is the methylation view.

## Config slots

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 |
| --- | --- |
| **threshold**<br>[`number`](https://jbrowse.org/jb2/docs/config_guides/slot_types#number) = <code>10</code> | hide a call whose probability is under this percent in the by-type view; the two-color view cuts at 50 and the methylation fill paints every cytosine |
| **twoColor**<br>[`boolean`](https://jbrowse.org/jb2/docs/config_guides/slot_types#boolean) = <code>false</code> | paint the unmodified side blue as well as the modified side its color, under modifications and bisulfite alike |
| **fillUnmarked**<br>[`boolean`](https://jbrowse.org/jb2/docs/config_guides/slot_types#boolean) = <code>false</code> | paint every cytosine in the context as methylated or unmethylated, the ones the basecaller left implicit included; the methylation view |
| **cytosineContext**<br>[`stringEnum`](https://jbrowse.org/jb2/docs/config_guides/slot_types#stringenum) = <code>'CG'</code> | which cytosines the methylation fill and bisulfite paint: CG, CHG, CHH or all |
| **shownModifications**<br>[`stringArray`](https://jbrowse.org/jb2/docs/config_guides/slot_types#stringarray) = <code>[]</code> | the modification type codes drawn (m, h, a, ...); empty draws every type the reads carry |