From 4a6d0e2a43261a3b4d4941dc9a867e32261c861c Mon Sep 17 00:00:00 2001 From: Riley Grant Date: Tue, 20 Aug 2024 14:23:45 -0500 Subject: [PATCH] fixup: fix misc. typos --- browser/help/topics/v4-browser-hts.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/browser/help/topics/v4-browser-hts.md b/browser/help/topics/v4-browser-hts.md index 946a242df..99ef00c46 100644 --- a/browser/help/topics/v4-browser-hts.md +++ b/browser/help/topics/v4-browser-hts.md @@ -32,7 +32,7 @@ Row fields: - `locus`: Variant locus. Contains contig and position information. - `alleles`: Variant alleles. - `exome`: Struct containing information about variant from exome data. - - `colocated_variants`: Struct containing array of variants located at ths same Locus as this variant, e.g. for the variant `1-55051215-G-GA`, the variants `1-55051215-G-A` and `1-55051215-G-T` are colocated. + - `colocated_variants`: Struct containing array of variants located at the same Locus as this variant, e.g. for the variant `1-55051215-G-GA`, the variants `1-55051215-G-A` and `1-55051215-G-T` are colocated. - `all`: An array containing colocated variants that are present in the entire exome dataset. - `non_ukb`: An array containing colocated variants that are present in the non-UK Biobank (UKB) subset of the dataset. - `subsets`: A set containing the subsets this variant is seen in. @@ -102,7 +102,7 @@ Row fields: - `faf95_joint`: A struct containing joint (exome + genome) FAF information (95% CI). - `grpmax`: Groupmax FAF value for all genetic ancestry groups across exomes + genomes. - `grpmax_gen_anc`: Genetic ancestry group associated with the value `grpmax` above. -- `faf99_joint`: A struct containing joint (exome + genome) FAF (99% CI). +- `faf99_joint`: A struct containing joint (exome + genome) FAF (99% CI). Contains same fields as `faf95_joint`. - `colocated_variants`: Array containing all variants (exome + genome) that are located at the same locus as this variant. - `coverage`: Struct containing coverage information for locus. - `exome`: Struct containing exome coverage information. @@ -121,14 +121,14 @@ Row fields: - `transcript_consequences`: Array containing variant transcript consequence information. - `biotype`: Transcript biotype. - `consequence_terms`: Array of predicted functional consequences. - - `domains`: Sset containing protein domains affected by variant. + - `domains`: Set containing protein domains affected by variant. - `gene_id`: Unique ID of gene associated with transcript. - `hgvsc`: HGVS coding sequence notation for variant. - `hgvsp`: HGVS protein notation for variant. - `is_canonical`: Whether transcript is the canonical transcript. - `lof_filter`: Variant LoF filters (from [LOFTEE](https://github.com/konradjk/loftee)). - `lof_flags`: LOFTEE flags. - - `lof`: Variant LOFTEE status (high confidence [HC] or low confidence [LC]). + - `lof`: Variant LOFTEE status (high confidence `HC` or low confidence `LC`). - `major_consequence`: Primary consequence associated with transcript. - `transcript_id`: Unique transcript ID. - `transcript_version`: Transcript version. @@ -137,7 +137,7 @@ Row fields: - `is_mane_select_version`: MANE Select version; has a value if this transcript is the MANE select transcript. - `refseq_id`: RefSeq ID associated with transcript. - `refseq_version`: RefSeq version. -- `caid`: The ClinGen Allele id associated with this variant. +- `caid`: The ClinGen Allele ID associated with this variant. - `vrs`: Struct containing information about this variant in accordance with the [Variant Representation (VRS)](https://vrs.ga4gh.org/en/stable/) standard. - `ref`: Struct containing information about the reference allele. - `allele_id`: The unique Allele ID. @@ -157,7 +157,7 @@ Row fields: - `strand`: Gene strand. - `start`: Gene genomic start position (position only). - `stop`: Gene genomic stop position (position only). -- `xstart`: Gene genomic start position (format: chromosomeposition). xpos can be calculated with ((chrom \* 109) + pos), note that chrX is encoded as 23, chrY as 24, and chrM as 25. e.g. `1-55051215` becomes `1055051215`, and `X:9786429` becomes `23009786429`. +- `xstart`: Gene genomic start position (format: chromosomeposition). xstart can be calculated with ((chrom \* 109) + pos), note that chrX is encoded as 23, chrY as 24, and chrM as 25. e.g. `1-55051215` becomes `1055051215`, and `X:9786429` becomes `23009786429`. - `xstop`: Gene genomic stop position (format: chromosomeposition). - `exons`: Array containing exon information for gene. - `feature_type`: Exon type (e.g., CDS). @@ -184,9 +184,9 @@ Row fields: - `xstart`: Exon genomic start position (format: chromsomeposition). - `xstop`: Exon genomic start position (format: chromsomeposition). - `reference_genome`: Reference genome associated with this transcript. - - `refseq_id`: Transcript RefSeq identifier. + - `refseq_id`: Transcript RefSeq ID. - `refseq_version`: RefSeq version. -- `hgnc_id`: HGNC gene identifier. +- `hgnc_id`: HGNC gene ID. - `symbol`: Gene symbol. - `name`: Gene name. - `previous_symbols`: Set containing previous gene symbols.