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) <noreply@anthropic.com>

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