44c00f07b0e94306e09f30c84ea6ab0f044e1a29
max
Fri Aug 14 05:09:12 2026 -0700
adding lin et al long-read SV subtrack, refs #38099
diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index b19c31b037b..11a432fa725 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -17,123 +17,124 @@
filter.svLen 0:250000000
filterByRange.svLen on
filterLabel.svLen SV Length (bp)
filter.insLen 0:30176500
filterByRange.insLen on
filterLabel.insLen Insertion Length (bp)
filter.AC 0:30000
filterByRange.AC on
filterLabel.AC Allele Count
noScoreFilter on
include lrSvAll.ra
track colorsDbSv
parent longReadVariants
+ priority 1
bigDataUrl /gbdb/$D/lrSv/colorsDb/sv.$D.bb
shortLabel CoLoRSdb 1427 SVs
- longLabel Structural Variants from CoLoRSdb (Consortium of Long-Read Sequencing, 1,427 Samples)
+ longLabel Structural Variants from 1,427 CoLoRSdb samples (Consortium of Long-Read Sequencing, PacBio HiFi)
type bigBed 9 +
itemRgb on
visibility hide
dataVersion v1.2.0
mouseOver Var: $name ($svType)
SV len: $svLen
Ins len: $insLen
AF: $AF
AC: $AC/$AN (Hom $acHom, Het $acHet, Hemi $acHemi)
Samples: $NS
filterValues.svType DEL,INS,INV,DUP
filterType.svType multipleListOr
filterLabel.svType SV Type
filter.svLen 0:101381
filterByRange.svLen on
filterLabel.svLen SV Length (bp)
filter.insLen 0:18724
filterByRange.insLen on
filterLabel.insLen Insertion Length (bp)
filter.AC 0:2854
filterByRange.AC on
filterLabel.AC Alt Allele Count (AC)
filter.AF 0:1
filterByRange.AF on
filterLimits.AF 0:1
filterLabel.AF Allele Frequency (AF)
skipEmptyFields on
- priority 1
track lrSv1kgOnt
parent longReadVariants
+ priority 4
bigDataUrl /gbdb/$D/lrSv/1kgOnt.bb
- shortLabel 1KG ONT 1019 SVs
- longLabel Structural Variants from 1000 Genomes Vienna ONT - 1,019 genomes (Schloissnig et al. 2025)
+ shortLabel 1KG Vienna ONT SVs
+ longLabel Structural Variants from 1,019 1000 Genomes samples (Vienna ONT; Schloissnig et al. 2025)
type bigBed 9 +
itemRgb on
visibility hide
mouseOver Var: $name ($svType)
SV len: $svLen
Ins len: $insLen
Type: $insType
Family: $family
AC: $AC
AF: $alleleFreq
filterValues.svType DEL,INS,CPX
filterType.svType multipleListOr
filterLabel.svType SV Type
filterValues.insType COMPLEX_DUP,DUP,DUP_INTERSPERSED,INV_DUP,NUMT,PSD,VNTR,chimera,orphan,partnered,solo
filterType.insType multipleListOr
filterLabel.insType Insertion/Deletion Type
filterValues.family Alu,HERVK,L1,LTR5_Hs,SVA
filterType.family multipleListOr
filterLabel.family Transposon Family
filter.svLen 0:49171
filterByRange.svLen on
filterLabel.svLen SV Length
filter.insLen 0:48091
filterByRange.insLen on
filterLabel.insLen Insertion Length
filterByRange.alleleFreq on
filterLimits.alleleFreq 0:1
filterLabel.alleleFreq Allele Frequency
filter.AC 0:1816
filterByRange.AC on
filterLabel.AC Allele Count
skipEmptyFields on
dataVersion 1.1
- priority 2
track gustafsonSv
parent longReadVariants
+ priority 5
bigDataUrl /gbdb/$D/lrSv/gustafson.bb
- shortLabel 1KG ONT UW 100 SVs
- longLabel Structural Variants from 1000 Genomes University of Washington ONT - 100 samples (Gustafson et al. 2024)
+ shortLabel 1KG UW ONT SVs
+ longLabel Structural Variants from 100 1000 Genomes samples (University of Washington ONT; Gustafson et al. 2024)
type bigBed 9 +
itemRgb on
visibility hide
mouseOver Var: $name ($svType)
SV len: $svLen
Ins len: $insLen
AC: $AC
Samples: $sampleCount
filterValues.svType DEL,INS,DUP,INV
filterType.svType multipleListOr
filterLabel.svType SV Type
filter.svLen 0:98289
filterByRange.svLen on
filterLabel.svLen SV Length
filter.insLen 0:25094
filterByRange.insLen on
filterLabel.insLen Insertion Length
filter.AC 0:200
filterByRange.AC on
filterLabel.AC Allele Count (placeholder)
filter.sampleCount 1:100
filterByRange.sampleCount on
filterLabel.sampleCount Number of Carrier Samples
skipEmptyFields on
- priority 3
track noyvertSv
parent longReadVariants
+ priority 6
bigDataUrl /gbdb/$D/lrSv/noyvert.bb
- shortLabel 1KG ONT Boehringer
- longLabel Structural Variants from 1000 Genomes ONT Boehringer - 888 Individuals (Noyvert et al. 2025)
+ shortLabel 1KG Boehringer ONT SVs
+ longLabel Structural Variants from 888 1000 Genomes samples (Boehringer ONT; Noyvert et al. 2025)
type bigBed 9 +
itemRgb on
visibility hide
mouseOver Var: ${name} (${svType})
SV len: ${svLen}
Ins len: ${insLen}
AF: ${AF}
AC: ${AC}/${AN}
GWAS hits: ${nGwas}
filterValues.svType DEL,INS,INV,DUP,BND
filterType.svType multipleListOr
filterLabel.svType SV Type
filter.svLen 0:28634664
filterByRange.svLen on
filterLabel.svLen SV Length (bp)
filter.insLen 0:45109
filterByRange.insLen on
filterLabel.insLen Insertion Length (bp)
filter.AC 0:1776
filterByRange.AC on
@@ -165,34 +166,34 @@
filter.nGwas 0:11
filterByRange.nGwas on
filterLabel.nGwas UK Biobank GWAS Hit Count
filter.r2Loo 0:1
filterByRange.r2Loo on
filterLimits.r2Loo 0:1
filterLabel.r2Loo Imputation r2 (leave-one-out)
filter.concordanceLoo 0:1
filterByRange.concordanceLoo on
filterLimits.concordanceLoo 0:1
filterLabel.concordanceLoo Minor Allele Concordance (leave-one-out)
skipEmptyFields on
track lrSv1kLin
parent longReadVariants
- release alpha
+ priority 3
bigDataUrl /gbdb/$D/lrSv/lin1218.bb
- shortLabel 1KG Merged 1218 SVs
- longLabel Structural Variants from 1000 Genomes merged - 1218 individuals (HiFi, ONT & assembly)
+ shortLabel 1KG Lin 1218 SVs
+ longLabel Structural Variants from 1,218 1000 Genomes samples (long-read merge; Lin et al.)
type bigBed 9 +
itemRgb on
visibility hide
mouseOver Var: $name ($svType)
SV len: $svLen
Ins len: $insLen
AC: $AC/$AN
AF: $AF
AF (African): $afAfr
AF (European): $afEur
Samples: $NS
filterValues.svType DEL,INS
filterType.svType multipleListOr
filterLabel.svType SV Type
filter.svLen 0:99565
filterByRange.svLen on
filterLabel.svLen SV Length (bp)
filter.insLen 0:99968
filterByRange.insLen on
filterLabel.insLen Insertion Length (bp)
filter.AC 0:2436
filterByRange.AC on
@@ -216,171 +217,177 @@
filter.afEur 0:1
filterByRange.afEur on
filterLimits.afEur 0:1
filterLabel.afEur AF European
filter.afSas 0:1
filterByRange.afSas on
filterLimits.afSas 0:1
filterLabel.afSas AF South Asian
filter.NS 1:1218
filterByRange.NS on
filterLabel.NS Samples with Genotype Data
skipEmptyFields on
track aou1kSv
parent longReadVariants
+ priority 2
bigDataUrl /gbdb/$D/lrSv/aou1k.bb
shortLabel AoU 1027 SVs
- longLabel Structural Variants from 1,027 AoU Individuals (PacBio HiFi Long-read)
+ longLabel Structural Variants from 1,027 All of Us samples (PacBio HiFi)
type bigBed 9 +
itemRgb on
visibility hide
mouseOver Var: $name ($svType)
SV len: $svLen
Ins len: $insLen
AC (approx): $AC
AF (African): $afAfr
AF (European): $afEur
filterValues.svType DEL,INS
filterType.svType multipleListOr
filterLabel.svType SV Type
filter.svLen 0:9905
filterByRange.svLen on
filterLabel.svLen SV Length
filter.insLen 0:9998
filterByRange.insLen on
filterLabel.insLen Insertion Length
filter.AC 0:2054
filterByRange.AC on
filterLabel.AC Allele Count (approx)
filterByRange.afAfr on
filterLimits.afAfr 0:1
filterLabel.afAfr AF African
filterByRange.afEur on
filterLimits.afEur 0:1
filterLabel.afEur AF European
filterByRange.afEas on
filterLimits.afEas 0:1
filterLabel.afEas AF East Asian
skipEmptyFields on
track han945Sv
parent longReadVariants
+ priority 12
bigDataUrl /gbdb/$D/lrSv/han945.bb
shortLabel Han 945 SVs
- longLabel Structural Variants from 945 Han Chinese (Long-read Sequencing)
+ longLabel Structural Variants from 945 Han Chinese samples (long-read)
type bigBed 9 +
itemRgb on
visibility hide
mouseOver Var: $name ($svType)
SV len: $svLen
Ins len: $insLen
AF: $alleleFreq
AC: $AC
Samples: $sampleCount
filterValues.svType DEL,INS,DUP,INV,TRA
filterType.svType multipleListOr
filterLabel.svType SV Type
filter.svLen 0:99743
filterByRange.svLen on
filterLabel.svLen SV Length
filter.insLen 0:27242
filterByRange.insLen on
filterLabel.insLen Insertion Length
filter.AC 0:1890
filterByRange.AC on
filterLabel.AC Allele Count (approx 2*SUPP)
filter.sampleCount 1:945
filterByRange.sampleCount on
filterLabel.sampleCount Number of Supporting Samples
filter.alleleFreq 0:1
filterByRange.alleleFreq on
filterLimits.alleleFreq 0:1
filterLabel.alleleFreq Allele Frequency
skipEmptyFields on
urls chr2="hgTracks?position=$$"
track tommoJpSv
parent longReadVariants
+ priority 14
bigDataUrl /gbdb/$D/lrSv/tommoJp.bb
shortLabel ToMMo 333 SVs
- longLabel Structural Variants from 333 Japanese Individuals (ToMMo, 111 Trios)
+ longLabel Structural Variants from 333 Japanese samples (ToMMo, 111 trios)
type bigBed 9 +
itemRgb on
visibility hide
mouseOver Var: $name ($svType)
SV len: $svLen
Ins len: $insLen
AF: $alleleFreq
AC: $AC
filterValues.svType DEL,INS
filterType.svType multipleListOr
filterLabel.svType SV Type
filter.svLen 0:99985
filterByRange.svLen on
filterLabel.svLen SV Length
filter.insLen 0:30649
filterByRange.insLen on
filterLabel.insLen Insertion Length
filter.alleleFreq 0:1
filterByRange.alleleFreq on
filterLimits.alleleFreq 0:1
filterLabel.alleleFreq Allele Frequency
filter.AC 0:444
filterByRange.AC on
filterLabel.AC Allele Count
track ga4kSv
parent longReadVariants
+ priority 16
bigDataUrl /gbdb/$D/lrSv/ga4kSv.bb
shortLabel GA4K 502 SVs
- longLabel Structural Variants from 502 Children's Mercy GA4K Probands (PacBio HiFi)
+ longLabel Structural Variants from 502 GA4K samples (Children's Mercy, pediatric rare disease; PacBio HiFi)
type bigBed 9 +
itemRgb on
visibility hide
mouseOver Var: $name ($svType)
SV len: $svLen
Ins len: $insLen
AC (approx): $AC
AF: $alleleFreq
Carriers: $carrierCount/$sampleTotal
filterValues.svType DEL,INS,DUP,INV
filterType.svType multipleListOr
filterLabel.svType SV Type
filter.svLen 0:809711
filterByRange.svLen on
filterLabel.svLen SV Length
filter.insLen 0:14923
filterByRange.insLen on
filterLabel.insLen Insertion Length
filter.AC 0:996
filterByRange.AC on
filterLabel.AC Allele Count (approx)
filter.alleleFreq 0:1
filterByRange.alleleFreq on
filterLimits.alleleFreq 0:1
filterLabel.alleleFreq Allele Frequency
filter.carrierCount 1:498
filterByRange.carrierCount on
filterLabel.carrierCount Number of Carrier Samples
track decodeSv
parent longReadVariants
+ priority 11
bigDataUrl /gbdb/$D/lrSv/decodeSv.bb
shortLabel deCODE 3622 SVs
- longLabel High-confidence Structural Variants from 3,622 Icelanders (deCODE, Oxford Nanopore)
+ longLabel Structural Variants from 3,622 deCODE samples (Icelandic; Oxford Nanopore)
type bigBed 9 +
itemRgb on
visibility hide
mouseOver Var: $name ($svType)
SV len: $svLen
Ins len: $insLen
filterValues.svType DEL,INS,INSDEL
filterType.svType multipleListOr
filterLabel.svType SV Type
filter.svLen 0:861080
filterByRange.svLen on
filterLabel.svLen SV Length
filter.insLen 0:22130
filterByRange.insLen on
filterLabel.insLen Insertion Length
skipEmptyFields on
track hprc2v21Sv
parent longReadVariants
+ priority 7
bigDataUrl /gbdb/$D/lrSv/hprc2v21.bb
shortLabel HPRC v2.1 233 SVs
- longLabel Structural Variants from HPRC v2.1 Pangenome Graph (233 samples, minigraph-cactus)
+ longLabel Structural Variants from 233 HPRC v2.1 assemblies (minigraph-cactus pangenome graph)
type bigBed 9 +
itemRgb on
visibility hide
mouseOver Var: $name ($svType)
SV len: $svLen
Ins len: $insLen
AF: $alleleFreq
AC: $AC/$alleleNumber
Samples: $nSamples
filterValues.svType INS,DEL
filterType.svType multipleListOr
filterLabel.svType SV Type
filter.svLen 0:99835
filterByRange.svLen on
filterLabel.svLen SV Length
filter.insLen 0:1064897
filterByRange.insLen on
filterLabel.insLen Insertion Length
filter.AC 0:463
filterByRange.AC on
@@ -424,66 +431,68 @@
#filterLimits.alleleFreq 0:1
#filterLabel.alleleFreq Carrier Frequency
#filter.nCallers 1:14
#filterByRange.nCallers on
#filterLabel.nCallers Number of Supporting Callers
#filterValues.callers DELLY,DeBreak,DeepVariant,PAV,SVDSS,SVIM,SVIM-asm,Sniffles2,cuteSV,cuteSV-asm,dipcall,longcallD,pbsv,sawfish
#filterType.callers multipleListAnd
#filterLabel.callers Supporting Callers
#filterValues.sources PAV,dipcall,longcallD
#filterType.sources multipleListAnd
#filterLabel.sources Source Pipeline
#skipEmptyFields on
track hgsvc2Sv
parent longReadVariants
+ priority 9
bigDataUrl /gbdb/$D/lrSv/hgsvc2.bb
shortLabel HGSVC2 32 SVs
- longLabel Structural Variants from 32 Haplotype-Resolved Genomes (HGSVC2 freeze 4, Ebert 2021)
+ longLabel Structural Variants from 32 HGSVC2 assemblies (freeze 4; Ebert et al. 2021)
type bigBed 9 +
itemRgb on
visibility hide
mouseOver Var: $name ($svType)
SV len: $svLen
Ins len: $insLen
Samples: $sampleCount
AC: $AC
AF: $popAllAf
filterValues.svType DEL,INS,INV
filterType.svType multipleListOr
filterLabel.svType SV Type
filter.svLen 0:57207414
filterByRange.svLen on
filterLabel.svLen SV Length
filter.insLen 0:108546
filterByRange.insLen on
filterLabel.insLen Insertion Length
filter.AC 1:35
filterByRange.AC on
filterLabel.AC Allele Count (carrier haplotypes)
filter.sampleCount 1:35
filterByRange.sampleCount on
filterLabel.sampleCount Sample Count
filterValues.refTrf True,False
filterType.refTrf multipleListOr
filterLabel.refTrf In Tandem Repeat
filter.refSd 0:1
filterByRange.refSd on
filterLimits.refSd 0:1
filterLabel.refSd Segmental Duplication Overlap
skipEmptyFields on
track hgsvc3Sv
parent longReadVariants
+ priority 8
bigDataUrl /gbdb/$D/lrSv/hgsvc3.bb
shortLabel HGSVC3 65 SVs
- longLabel Structural Variants from 65 Diverse Samples (HGSVC3 ONT+HIFI)
+ longLabel Structural Variants from 65 HGSVC3 assemblies (diverse ancestry; HiFi + ONT)
type bigBed 9 +
itemRgb on
visibility hide
mouseOver Var: $name ($svType)
SV len: $svLen
Ins len: $insLen
Samples: $sampleCount
AC: $AC
filterValues.svType DEL,INS,INV
filterType.svType multipleListOr
filterLabel.svType SV Type
filter.svLen 0:30176500
filterByRange.svLen on
filterLabel.svLen SV Length
filter.insLen 0:30176500
filterByRange.insLen on
filterLabel.insLen Insertion Length
filter.AC 1:136
filterByRange.AC on
@@ -537,108 +546,112 @@
filterByRange.afHc on
filterLimits.afHc 0:1
filterLabel.afHc Allele Frequency (HC)
filter.afIlbd 0:1
filterByRange.afIlbd on
filterLimits.afIlbd 0:1
filterLabel.afIlbd Allele Frequency (ILBD)
filter.differentialRate -1:1
filterByRange.differentialRate on
filterLimits.differentialRate -1:1
filterLabel.differentialRate Case-Control Differential (case - control)
skipEmptyFields on
track aprSv
parent longReadVariants
+ priority 15
bigDataUrl /gbdb/$D/lrSv/apr.bb
shortLabel Arab APR 53 SVs
- longLabel Structural Variants from the Arab Pangenome Reference (53 UAE-resident Arab samples)
+ longLabel Structural Variants from 53 Arab Pangenome Reference samples (UAE-resident; HiFi + ONT)
type bigBed 9 +
itemRgb on
visibility hide
mouseOver Var: $name ($svType)
SV len: $svLen
Ins len: $insLen
AC: $AC/$alleleNumber
AF: $alleleFreq
Samples: $numSamples
Alts: $numAlts
filterValues.svType INS,DEL,CPX,MIXED
filterType.svType multipleListOr
filterLabel.svType SV Type
filter.svLen 0:99885
filterByRange.svLen on
filterLabel.svLen SV Length
filter.insLen 0:584016
filterByRange.insLen on
filterLabel.insLen Insertion Length
filter.AC 0:107
filterByRange.AC on
filterLabel.AC Allele Count
filterByRange.alleleFreq on
filterLimits.alleleFreq 0:1
filterLabel.alleleFreq Allele Frequency
skipEmptyFields on
track cpc1Sv
parent longReadVariants
+ priority 13
bigDataUrl /gbdb/$D/lrSv/cpc1.bb
shortLabel CPC 58 SVs
- longLabel Structural Variants from the Chinese Pangenome Consortium (58 samples, CPC-only)
+ longLabel Structural Variants from 58 Chinese Pangenome Consortium samples (CPC-only; HiFi)
type bigBed 9 +
itemRgb on
visibility hide
mouseOver Var: $name ($svType)
SV len: $svLen
Ins len: $insLen
AC: $AC/$alleleNumber
AF: $alleleFreq
Samples: $numSamples
Alts: $numAlts
filterValues.svType INS,DEL,CPX,MIXED
filterType.svType multipleListOr
filterLabel.svType SV Type
filter.svLen 0:8998096
filterByRange.svLen on
filterLabel.svLen SV Length
filter.insLen 0:376583
filterByRange.insLen on
filterLabel.insLen Insertion Length
filter.AC 0:116
filterByRange.AC on
filterLabel.AC Allele Count
filterByRange.alleleFreq on
filterLimits.alleleFreq 0:1
filterLabel.alleleFreq Allele Frequency
skipEmptyFields on
track chirmade101Sv
parent longReadVariants
+ priority 17
bigDataUrl /gbdb/$D/lrSv/chirmade101.bb
shortLabel SVatalog 101 SVs
- longLabel Structural Variants from 101 Long-read WGS (GWAS SVatalog, Chirmade 2026)
+ longLabel Structural Variants from 101 SVatalog samples (cystic fibrosis; Chirmade et al. 2026)
type bigBed 9 +
itemRgb on
visibility hide
mouseOver Var: $name ($svType)
SV len: $svLen
Ins len: $insLen
Genes: $geneCount
filterValues.svType DEL,INS,DUP,INV,CPX
filterType.svType multipleListOr
filterLabel.svType SV Type
filter.svLen 0:1321484
filterByRange.svLen on
filterLabel.svLen SV Length
filter.insLen 0:31711
filterByRange.insLen on
filterLabel.insLen Insertion Length
filter.geneCount 0:200
filterByRange.geneCount on
filterLabel.geneCount Gene Count
skipEmptyFields on
track cardSv
parent longReadVariants
+ priority 10
bigDataUrl /gbdb/$D/lrSv/card.bb
shortLabel CARD 351 SVs
- longLabel Structural Variants from 351 Brain Samples (NIH CARD Long-read ONT, NABEC + HBCC)
+ longLabel Structural Variants from 351 NIH CARD brain samples (ONT; NABEC + HBCC)
type bigBed 9 +
itemRgb on
visibility hide
mouseOver Var: ${name} (${svType})
SV len: ${svLen}
Ins len: ${insLen}
AF: ${alleleFreq}
AC: ${AC} (NABEC ${nabecAc}, HBCC ${hbccAc})
filterValues.svType DEL,INS,INV,DUP
filterType.svType multipleListOr
filterLabel.svType SV Type
filter.svLen 0:30282742
filterByRange.svLen on
filterLabel.svLen SV Length
filter.insLen 0:92867161
filterByRange.insLen on
filterLabel.insLen Insertion Length
filter.AC 0:702
filterByRange.AC on