efebc8a0a29aeef60bc470a40ced7a2aa6652efd lrnassar Tue Sep 8 19:25:02 2026 -0700 Adding native mm10 track for the mouse strains Cactus alignment. refs #38308 New alpha-gated track mouseStrainsCactus exposing the Progressive Cactus alignment of the 16 Mouse Genomes Project strain assemblies plus rat, which until now was only reachable by attaching the mouseStrains assembly hub. bigDataUrl, summary and frames point at the existing bigMaf files on hgdownload rather than copying 8.8 GB into /gbdb, the same way the hg38 cactus241wayBM track is served. Polish over the hub stanza: renamed from the generic "bigMaf", off by default, speciesGroups splitting the strains into wild-derived, classical laboratory and Rat/rn6, speciesLabels so side labels read 129S1/SvImJ rather than 129S1_SvImJ, plus treeImage and speciesCodonDefault. The three new sGroup_ tags are registered in tagTypes.tab. Description page written from Lilue et al. 2018; the hub page had an empty Description section and its Display Convention text was wigMaf boilerplate that did not match this track. Also notes that the alignment is a poor source for large rearrangements, since Ragout built the strain pseudo-chromosomes against the reference and discarded most adjacencies that disagreed with it. Added a reciprocal relatedTracks.ra pair between this track and mm10Strains1 ("Alternate strains"), since #38227 came in from a user who kept landing on mm10Strains1 while looking for this alignment. Co-Authored-By: Claude Opus 5 (1M context) diff --git src/hg/makeDb/trackDb/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra index 62c7ece2f1f..d17d858d705 100644 --- src/hg/makeDb/trackDb/relatedTracks.ra +++ src/hg/makeDb/trackDb/relatedTracks.ra @@ -598,15 +598,19 @@ hg38 constraintSuper predictionScoresSuper Per-variant deleteriousness and pathogenicity scores, rather than regional constraint hg38 predictionScoresSuper constraintSuper Regional and gene-level constraint measured from population variation hg38 ~jarvis ukbDepletion Another score for how depleted of variation a non-coding region is hg38 ~hmc gnomadPLI Another constraint metric derived from the absence of variation in population data hg38 hmc ucscGenePfam The Pfam domains that homologous missense constraint is calculated over hg38 ucscGenePfam hmc Missense constraint measured across homologous positions within these domains hg38 promoterAi jarvis A score prioritizing non-coding regions more broadly, not only promoters hg38 jarvis promoterAi A deep-learning predictor for variants in promoter regions specifically hg19 constraintSuper predictionScoresSuper Per-variant deleteriousness and pathogenicity scores, rather than regional constraint hg19 predictionScoresSuper constraintSuper Regional and gene-level constraint measured from population variation hg19 ~jarvis ukbDepletion Another score for how depleted of variation a non-coding region is hg19 ~hmc gnomadPLI Another constraint metric derived from the absence of variation in population data hg19 hmc ucscGenePfam The Pfam domains that homologous missense constraint is calculated over hg19 ucscGenePfam hmc Missense constraint measured across homologous positions within these domains + +# mm10 mouse strain cross-links: +mm10 mm10Strains1 mouseStrainsCactus Whole-genome alignment of the 16 strain assemblies to the reference +mm10 mouseStrainsCactus mm10Strains1 Alternate strain sequences mapped to their reference genome location