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fix(docs): display everything on the mutation filters page
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fengelniederhammer committed Jan 9, 2024
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22 changes: 12 additions & 10 deletions lapis2-docs/src/content/docs/concepts/mutation-filters.md
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Expand Up @@ -3,16 +3,18 @@ title: Mutation filters
description: Mutation filters
---

It is possible to filter for amino acid and nucleotide bases/mutations. Multiple mutations can be provided by specifying
a comma-separated list.
It is possible to filter for amino acid and nucleotide bases/mutations.
Multiple mutations can be provided by specifying a comma-separated list.

A nucleotide mutation has the format <position><base>. A "base" can be one of the four nucleotides A, T, C, and G. It
can also be - for deletion and N for unknown.
A nucleotide mutation has the format `<position><base>`.
A `<base>` can be one of the four nucleotides `A`, `T`, `C`, and `G`.
It can also be `-` for deletion and `N` for unknown.

An amino acid mutation has the format <gene>:<position><base>. The following genes are available: E, M, N, ORF1a, ORF1b,
ORF3a, ORF6, ORF7a, ORF7b, ORF8, ORF9b, S. A "base" can be one of the 20 amino acid codes. It can also be - for deletion
and X for unknown.
An amino acid mutation has the format `<gene>:<position><base>`.
The following genes are available: E, M, N, ORF1a, ORF1b, ORF3a, ORF6, ORF7a, ORF7b, ORF8, ORF9b, S.
A `<base>` can be one of the 20 amino acid codes.
It can also be `-` for deletion and `X` for unknown.

The <base> can be omitted to filter for any mutation. You can write a `.` for the <base> to filter for sequences for
which it is confirmed that no mutation occurred, i.e., has the same base as the reference genome at the specified
position.
The `<base>` can be omitted to filter for any mutation.
You can write a `.` for the `<base>` to filter for sequences for which it is confirmed that no mutation occurred,
i.e. has the same base as the reference genome at the specified position.

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