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/mouse/mm10/trackDb.ra src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
index 9177e1b5281..5cab444849c 100644
--- src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
+++ src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
@@ -63,30 +63,31 @@
 color 20,20,170
 type bed 12
 
 track xenoClinvar
 shortLabel Human Variants
 longLabel ClinVar Variants mapped to Mouse
 type bigBed 9 +
 itemRgb on
 bigDataUrl /gbdb/mm10/bbi/xenoClinvar.bb
 group x
 mouseOverField _mouseOver
 urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" geneId="https://www.ncbi.nlm.nih.gov/gene/$$" snpId="https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/"
 release alpha
 
 include mm10Strains1SuperTrack.ra
+include mouseStrainsCactus.ra alpha
 
 track qPcrPrimers override
 group regulation
 url http://www.weizmann.ac.il/cgi-bin/USERcompphys/primers/mouse/extract_primer_by_line.cgi?$$
 urlLabel Click here for primer details:
 
 track ucscRetroAli2
 shortLabel Retroposed Genes
 longLabel Retroposed Genes V2, Including Pseudogenes
 group genes
 type psl
 color 20,0,250
 visibility hide
 ucscRetroInfo ucscRetroInfo2
 baseColorDefault diffCodons