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
@@ -1,435 +1,436 @@
 include ../../crispr10K.ra
 
 include knownGene.ra
 
 # chainNet tracks
 include trackDb.gliresChainNet.ra
 include trackDb.euarchontoglireChainNet.ra
 include trackDb.placentalsChainNet.ra
 include trackDb.vertebrateChainNet.ra
 include trackDb.previousVersionsChainNet.ra alpha
 include tabulaMurisSenis.ra
 include tabulamuris.ra
 include mouseDevTimecourse.ra
 include developmentTimecourseSignalMm10.ra
 include liftOverMm39.ra
 
 # Local declaration so that local gold.html is picked up.
 track gold override
 html gold
 
 # Local declaration so that local gap.html is picked up.
 track gap override
 html gap
 
 # Local declaration so that patents are in the right group
 track patSeq override
 group pub
 
 track patNonBulk override
 group pub
 
 track patBulk override
 group pub
 
 track assemblyFrags
 shortLabel Contigs
 longLabel Contig fragments used in the assembly
 group map
 visibility hide
 colorByStrand 150,100,30 100,50,0
 type bed 6
 urlLabel NCBI Nucleotide:
 url https://www.ncbi.nlm.nih.gov/nuccore/$$
 
 # different type of gold search here so the fragments can be found with
 #	or without their trailing .1
 searchTable gold
 searchMethod prefix
 searchType bed
 shortCircuit 1
 termRegex [ACGJ][ACLHRTY][A0-9]+(\.[0-9]+)?
 query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%'
 searchPriority 8
 
 include trackDb.60way.ra
 include trackDb.4way.ra alpha
 
 track mm9UcscGenes
 shortLabel mm9 Ucsc Genes
 longLabel  mm9 Ucsc Genes
 group genes
 visibility hide
 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
 baseColorUseCds table ucscRetroCds2
 baseColorUseSequence extFile ucscRetroSeq2 ucscRetroExtFile2
 indelDoubleInsert on
 indelQueryInsert on
 showDiffBasesAllScales .
 showDiffBasesMaxZoom 10000.0
 showCdsAllScales .
 showCdsMaxZoom 10000.0
 dataVersion Apr. 2013
 
 searchName ucscRetroInfoRefSeq2
 searchTable ucscRetroAli2
 searchDescription Retroposed Genes V2, Including Pseudogenes
 query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
 xrefTable hgFixed.refLink, ucscRetroInfo2
 dontCheckXrefQueryFormat 1
 xrefQuery select ucscRetroInfo2.name, hgFixed.refLink.name from %s where hgFixed.refLink.name like '%s%%' and refSeq = mrnaAcc 
 searchPriority 3.52
 
 searchName ucscRetroInfoMrna2
 searchTable ucscRetroAli2
 searchDescription Retroposed Genes V2, Including Pseudogenes
 query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
 searchPriority 3.55
 
 searchName ucscRetroUniProt2
 searchTable ucscRetroAli2
 searchDescription Retroposed Genes V2, Including Pseudogenes
 query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
 dontCheckXrefQueryFormat 1
 xrefTable kgXref, ucscRetroInfo2
 xrefQuery select ucscRetroInfo2.name, spDisplayID from %s where spDisplayID like '%s%%' and kgName = kgID 
 searchPriority 3.54
 
 searchName ucscRetroKnownGene2
 searchTable ucscRetroAli2
 searchDescription Retroposed Genes V2, Including Pseudogenes
 query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
 dontCheckXrefQueryFormat 1
 xrefTable kgXref, ucscRetroInfo2
 xrefQuery select ucscRetroInfo2.name, geneSymbol from %s where geneSymbol like '%s%%' and kgName = kgID 
 searchPriority 3.53
 
 track ucscRetroAli4
 shortLabel Retroposed Genes 4.0
 longLabel Retroposed Genes V4, Including Pseudogenes
 group genes
 type psl
 color 20,0,250
 visibility hide
 ucscRetroInfo ucscRetroInfo4
 baseColorDefault diffCodons
 baseColorUseCds table ucscRetroCds4
 baseColorUseSequence extFile ucscRetroSeq4 ucscRetroExtFile4
 indelDoubleInsert on
 indelQueryInsert on
 showDiffBasesAllScales .
 showDiffBasesMaxZoom 10000.0
 showCdsAllScales .
 showCdsMaxZoom 10000.0
 dataVersion Feb. 2014
 
 searchName ucscRetroInfoRefSeq4
 searchTable ucscRetroAli4
 searchDescription Retroposed GenesV4, Including Pseudogenes
 query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
 xrefTable hgFixed.refLink, ucscRetroInfo4
 dontCheckXrefQueryFormat 1
 xrefQuery select ucscRetroInfo4.name, hgFixed.refLink.name from %s where hgFixed.refLink.name like '%s%%' and refSeq = mrnaAcc 
 searchPriority 3.52
 
 searchName ucscRetroInfoMrna4
 searchTable ucscRetroAli4
 searchDescription Retroposed GenesV4, Including Pseudogenes
 query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
 searchPriority 3.55
 
 searchName ucscRetroUniProt4
 searchTable ucscRetroAli4
 searchDescription Retroposed GenesV4, Including Pseudogenes
 query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
 dontCheckXrefQueryFormat 1
 xrefTable kgXref, ucscRetroInfo4
 xrefQuery select ucscRetroInfo4.name, spDisplayID from %s where spDisplayID like '%s%%' and kgName = kgID 
 searchPriority 3.54
 
 searchName ucscRetroKnownGene4
 searchTable ucscRetroAli4
 searchDescription Retroposed GenesV4, Including Pseudogenes
 query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
 dontCheckXrefQueryFormat 1
 xrefTable kgXref, ucscRetroInfo4
 xrefQuery select ucscRetroInfo4.name, geneSymbol from %s where geneSymbol like '%s%%' and kgName = kgID 
 searchPriority 3.53
 
 track ucscRetroAli5
 shortLabel Retroposed Genes 5.0
 longLabel Retroposed Genes V5, Including Pseudogens
 group genes
 type psl
 color 20,0,250
 visibility hide
 ucscRetroInfo ucscRetroInfo5
 baseColorDefault diffCodons
 baseColorUseCds table ucscRetroCds5
 baseColorUseSequence extFile ucscRetroSeq5 ucscRetroExtFile5
 indelDoubleInsert on
 indelQueryInsert on
 showDiffBasesAllScales .
 showDiffBasesMaxZoom 10000.0
 showCdsAllScales .
 showCdsMaxZoom 10000.0
 dataVersion Jul. 2014
 
 searchName ucscRetroInfoRefSeq5
 searchTable ucscRetroAli5
 searchDescription Retroposed GenesV5, Including Pseudogenes - 2014-07-22
 query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
 xrefTable hgFixed.refLink, ucscRetroInfo5
 dontCheckXrefQueryFormat 1
 xrefQuery select ucscRetroInfo5.name, hgFixed.refLink.name from %s where hgFixed.refLink.name like '%s%%' and refSeq = mrnaAcc 
 searchPriority 3.52
 
 searchName ucscRetroInfoMrna5
 searchTable ucscRetroAli5
 searchDescription Retroposed GenesV5, Including Pseudogenes - 2014-07-22
 query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
 searchPriority 3.55
 
 searchName ucscRetroUniProt5
 searchTable ucscRetroAli5
 searchDescription Retroposed GenesV5, Including Pseudogenes - 2014-07-22
 query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
 dontCheckXrefQueryFormat 1
 xrefTable kgXref, ucscRetroInfo5
 xrefQuery select ucscRetroInfo5.name, spDisplayID from %s where spDisplayID like '%s%%' and kgName = kgID 
 searchPriority 3.54
 
 searchName ucscRetroKnownGene5
 searchTable ucscRetroAli5
 searchDescription Retroposed GenesV5, Including Pseudogenes - 2014-07-22
 query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
 dontCheckXrefQueryFormat 1
 xrefTable kgXref, ucscRetroInfo5
 xrefQuery select ucscRetroInfo5.name, geneSymbol from %s where geneSymbol like '%s%%' and kgName = kgID 
 searchPriority 3.53
 
 track ucscRetroAli6
 shortLabel RetroGenes V6
 longLabel Retroposed Genes V6, Including Pseudogenes
 group genes
 type psl
 color 20,0,250
 visibility hide
 ucscRetroInfo ucscRetroInfo6
 baseColorDefault diffCodons
 baseColorUseCds table ucscRetroCds6
 baseColorUseSequence extFile ucscRetroSeq6 ucscRetroExtFile6
 indelDoubleInsert on
 indelQueryInsert on
 showDiffBasesAllScales .
 showDiffBasesMaxZoom 10000.0
 showCdsAllScales .
 showCdsMaxZoom 10000.0
 dataVersion Jan. 2015
 exonNumbers off
 
 searchName ucscRetroInfoRefSeq6
 searchTable ucscRetroAli6
 searchDescription Retroposed Genes V6, Including Pseudogene
 query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
 xrefTable hgFixed.refLink, ucscRetroInfo6
 dontCheckXrefQueryFormat 1
 xrefQuery select ucscRetroInfo6.name, hgFixed.refLink.name from %s where hgFixed.refLink.name like '%s%%' and refSeq = mrnaAcc 
 searchPriority 3.52
 
 searchName ucscRetroInfoMrna6
 searchTable ucscRetroAli6
 searchDescription Retroposed Genes V6, Including Pseudogenes
 query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
 searchPriority 3.55
 
 searchName ucscRetroUniProt6
 searchTable ucscRetroAli6
 searchDescription Retroposed Genes V6, Including Pseudogenes
 query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
 dontCheckXrefQueryFormat 1
 xrefTable kgXref, ucscRetroInfo6
 xrefQuery select ucscRetroInfo6.name, spDisplayID from %s where spDisplayID like '%s%%' and kgName = kgID 
 searchPriority 3.54
 
 searchName ucscRetroKnownGene6
 searchTable ucscRetroAli6
 searchDescription Retroposed Genes V6, Including Pseudogenes
 query select tName, tStart,tEnd, qName from %s where qName like '%s%%'
 dontCheckXrefQueryFormat 1
 xrefTable kgXref, ucscRetroInfo6
 xrefQuery select ucscRetroInfo6.name, geneSymbol from %s where geneSymbol like '%s%%' and kgName = kgID 
 searchPriority 3.53
 
 track jaxQtl override
 shortLabel MGI QTL 
 longLabel Mouse Genome Informatics Quantitative Trait Loci ***Lifted from NCBI 37 (mm9)***
 origAssembly mm9 
 pennantIcon 9.jpg ../goldenPath/help/liftOver.html "These data were converted via liftOver from the July 2007 (NCBI37/mm9) version of the track"
 
 track FaceBase24SampleTypesAvg override
 origAssembly mm9
 pennantIcon 9.jpg ../goldenPath/help/liftOver.html "These data were converted via liftOver from the July 2007 (NCBI37/mm9) version of the track"
 
 track rmskJoinedBaseline override
 group varRep
 
 include trackDb.gencode.ra
 
 include defaultPriority.ra
 
 searchTable sgpGene
 searchType genePred
 termRegex chr[0-9MUXYn]+[GHJLv0-9_]+(alt_|random_)?[0-9]+(\.[0-9]+)?
 searchPriority 50
 
 searchTable geneid
 searchType genePred
 searchMethod prefix
 termRegex chr[0-9MUXYn]+[GHJLv0-9_]+(alt_|random_)?[0-9]+(\.[0-9]+)?
 searchPriority 50
 
 track strainSNPs
 shortLabel Mouse SNPs
 longLabel Annotated SNPs from mouse strain comparison analysis
 group varRep
 type vcfTabix
 visibility hide
 priority 11.5
 hapClusterHeight 360
 hapClusterEnabled on
 hapClusterMethod fileOrder
 maxWindowToDraw 1000000
 
 track nestedRepeats override
 group varRep
 priority 10
 
 track microsat override
 group varRep
 priority 11
 
 track genomicSuperDups override
 group varRep
 
 track simpleRepeat override
 group varRep
 
 track windowmaskerSdust override
 group varRep
 
 track spMut override
 group pub
 bigDataUrl /gbdb/$D/uniprot/unipMut.bb
 
 #######################3
 # regulation tracks
 
 include trackDb.encode3.ra beta,public
 include trackDb.encode3.alpha.ra alpha
 include encode3RenEnhancerGene.ra
 include encode.cCREs.override.ra
 include encode4Reg.ra
 include fantom5.ra
 include singleCellSignalsPeaks.ra alpha
 
 track epdNew
 compositeTrack on
 shortLabel EPDnew Promoters
 longLabel Promoters from EPDnew
 html ../../epdNewPromoter
 type bigBed 8
 group regulation
 visibility hide
 urlLabel EPDnew link:
 bedNameLabel Promoter ID
 exonArrows on
 
     track epdNewPromoter
     shortLabel EPDnew v6
     longLabel Promoters from EPDnew mouse version 003
     parent epdNew on
     bigDataUrl /gbdb/$D/bbi/epdNewMouse003.$D.bb
     dataVersion EPDNew Mouse Version 003 (June 2018)
     url https://epd.epfl.ch/cgi-bin/get_doc?db=mmEpdNew&format=genome&entry=$$
     color 50,50,200
     priority 1
 
     track epdNewPromoterNonCoding
     shortLabel EPDnew NC v1
     longLabel ncRNA promoters from EPDnewNC mouse version 001
     parent epdNew on
     bigDataUrl /gbdb/$D/bbi/epdNewMouseNc001.$D.bb
     dataVersion EPDNewNC Mouse Version 001 (August 2019)
     url https://epd.epfl.ch/cgi-bin/get_doc?db=mmNCEpdNew&format=genome&entry=$$
     color 180,0,134
     priority 2
 
 include dbSnpArchiveMm10.ra
 include reMap.ra
 
 track allGaps
 shortLabel All Gaps
 longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps
 group map
 visibility dense
 type bigBed 3
 bigDataUrl /gbdb/mm10/bbi/allGaps.bb
 html allGaps
 
 track vistaEnhancersBb
 shortLabel VISTA Enhancers
 longLabel VISTA Enhancers
 group regulation
 url https://enhancer.lbl.gov/vista/element?vistaId=$$
 type bigBed 9 +
 mouseOverField patternExpression
 urlLabel View on the VISTA Enhancer Browser
 bigDataUrl /gbdb/mm10/vistaEnhancers/vistaEnhancers.bb
 itemRgb on
 
 include ../../trackDb.mgc-orfeome.ra
 include ../refSeqComposite.mm10.mm39.ra
 
 include recount3.ra
 
 include long_read_transcripts.ra
 
 track ucscGenePfam override
 shortLabel Pfam in GENCODE
 longLabel Pfam Domains in GENCODE Genes
 html gencodePfam
 
 track jaspar2024 override
 parent jaspar on
 
 include tad.ra alpha