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Add description for low coverage and low MQ flags #1848

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7da9c2a
add note about two new gene flags to help page
ch-kr Feb 17, 2026
6ea8070
add newline
ch-kr Feb 17, 2026
14d763b
Update browser/help/faq/technical-details/what-do-the-flags-on-the-br…
ch-kr Feb 18, 2026
bc9b3a7
Update snapshot for gene flags page
phildarnowsky-broad Feb 19, 2026
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5 changes: 5 additions & 0 deletions browser/help/faq/technical-details/what-do-the-flags-on-the-browser-mean.md
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Expand Up @@ -25,3 +25,8 @@ Flags that will appear in the variant table on gene/region pages:
- NC Transcript: Marked in a putative LoF category by VEP (essential splice, stop-gained, or frameshift) but appears on a non-protein-coding transcript
- SEGDUP: Found in a region overlapping a segmental duplication (regions provided by GA4GH Benchmarking Team)
- Common low heteroplasmy: Variant is present at an overall frequency of .001 across all samples with a heteroplasmy level > 0 and < 0.50 (mitochondrial variants only)

Flags that will appear at the top of gene/transcript pages:

- Low exome coverage: Less than 10% of the coding base pairs in this gene are well-covered in the gnomAD exomes. Well-covered is defined here has having a median allele number percent (AN%; percent of total possible AN observed at site) greater than 90%
- Low exome mapping quality: The mean `AS_MQ` (allele-specific root mean square of the mapping quality of reads across all samples) value across this gene is less than 50
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