fcb3dd044df301a3c0ea4588e1debf7068b00333 lrnassar Mon Jun 29 15:43:06 2026 -0700 lrSv: fresh-eyes audit fixes + multi-line HTML mouseOvers on all subtracks. refs #36258 Audit fixes: - lrSv.html summary table: recompute the per-dataset min/median/max SV-length columns from current data (length = max(svLen,insLen)); the old values came from the .ra filter bounds and were off by one in several rows. Fixes the stale lrSvAll Max (190,088,223 -> 57,207,413, left over from before KimPD was dropped from the merge) and the APR row's length convention. - decodeSv.html: align the opening Description to the displayed (deduped) counts (119,453 / 41,216 DEL) instead of the upstream release counts, noting the dedup from the 133,886-record release. - Drop dead svType filter options (CNV/BND/MEI/CTX) that appear in no subtrack, from the lrSv supertrack filterValues.svType and from lrSvAll (both the generated lrSvAll.ra and the lrSvMergeAll.py generator). Reformat the mouseOver of all 16 subtracks to the same multi-line bold-label HTML style as lrSvAll (Var / SV len / Ins len / per-track fields), using each track's existing fields. diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra index 6e060aa567d..bbf9433b952 100644 --- src/hg/makeDb/trackDb/human/lrSv.ra +++ src/hg/makeDb/trackDb/human/lrSv.ra @@ -1,559 +1,559 @@ track lrSv superTrack on shortLabel Long-read SVs longLabel Structural Variants from Long-read Sequencing group varRep visibility hide # Supertrack-level filters. These are rendered on the supertrack's own # hgTrackUi page (superTrackUi in hgTrackUi.c). Cart values stored under # "lrSv.filter.<field>.min/max" are inherited at read time by every # subtrack via cartOptionalStringClosestToHome() walking tdb->parent. A # subtrack-level filter always wins over the supertrack-level one. -filterValues.svType DEL|DEL (Deletion),INS|INS (Insertion),INV|INV (Inversion),CPX|CPX (Complex rearrangement),DUP|DUP (Duplication),CNV|CNV (Copy-number variant),CTX|CTX (Chromosomal translocation),INSDEL|INSDEL (Insertion-deletion),MIXED|MIXED (multi-allele snarl),BND|BND (Breakend / translocation),MEI|MEI (Mobile element insertion),TRA|TRA (Translocation) +filterValues.svType DEL|DEL (Deletion),INS|INS (Insertion),INV|INV (Inversion),CPX|CPX (Complex rearrangement),DUP|DUP (Duplication),INSDEL|INSDEL (Insertion-deletion),MIXED|MIXED (multi-allele snarl),TRA|TRA (Translocation) filterType.svType multipleListOr filterLabel.svType SV Type 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 lrSv 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) type bigBed 9 + itemRgb on visibility hide dataVersion v1.2.0 - mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$AF AC=$AC/$AN (Hom:$acHom Het:$acHet Hemi:$acHemi) samples=$NS + mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AF</b>: $AF<br><b>AC</b>: $AC/$AN (Hom $acHom, Het $acHet, Hemi $acHemi)<br><b>Samples</b>: $NS filterValues.svType DEL,INS,INV,DUP filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:101381 filterByRange.svLen on filterLabel.svLen SV Length (bp) filter.insLen 0:18724 filterByRange.insLen on filterLabel.insLen Insertion Length (bp) filter.AC 0:2854 filterByRange.AC on filterLabel.AC Alt Allele Count (AC) filter.AF 0:1 filterByRange.AF on filterLimits.AF 0:1 filterLabel.AF Allele Frequency (AF) skipEmptyFields on priority 1 track lrSv1kgOnt parent lrSv bigDataUrl /gbdb/$D/lrSv/1kgOnt.bb shortLabel 1KG ONT 1019 SVs longLabel Structural Variants from 1,019 Diverse Humans (Vienna ONT, Schloissnig et al. 2025) type bigBed 9 + itemRgb on visibility hide - mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen type=$insType family=$family AC=$AC AF=$alleleFreq + mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>Type</b>: $insType<br><b>Family</b>: $family<br><b>AC</b>: $AC<br><b>AF</b>: $alleleFreq filterValues.svType DEL,INS,CPX filterType.svType multipleListOr filterLabel.svType SV Type filterValues.insType COMPLEX_DUP,DUP,DUP_INTERSPERSED,INV_DUP,NUMT,PSD,VNTR,chimera,orphan,partnered,solo filterType.insType multipleListOr filterLabel.insType Insertion/Deletion Type filterValues.family Alu,HERVK,L1,LTR5_Hs,SVA filterType.family multipleListOr filterLabel.family Transposon Family filter.svLen 0:49171 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:48091 filterByRange.insLen on filterLabel.insLen Insertion Length filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency filter.AC 0:1816 filterByRange.AC on filterLabel.AC Allele Count skipEmptyFields on dataVersion 1.1 priority 2 track gustafsonSv parent lrSv bigDataUrl /gbdb/$D/lrSv/gustafson.bb shortLabel 1KG ONT 100 SVs longLabel Structural Variants from 100 1000 Genomes ONT Samples (Gustafson et al. 2024) type bigBed 9 + itemRgb on visibility hide - mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC samples=$sampleCount + mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC</b>: $AC<br><b>Samples</b>: $sampleCount filterValues.svType DEL,INS,DUP,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:98289 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:25094 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:200 filterByRange.AC on filterLabel.AC Allele Count (placeholder) filter.sampleCount 1:100 filterByRange.sampleCount on filterLabel.sampleCount Number of Carrier Samples skipEmptyFields on priority 3 track aou1kSv parent lrSv bigDataUrl /gbdb/$D/lrSv/aou1k.bb shortLabel AoU 1027 SVs longLabel Structural Variants from 1,027 AoU Individuals (PacBio HiFi Long-read) type bigBed 9 + itemRgb on visibility hide - mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC~$AC AF_AFR=$afAfr AF_EUR=$afEur + mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC (approx)</b>: $AC<br><b>AF (African)</b>: $afAfr<br><b>AF (European)</b>: $afEur filterValues.svType DEL,INS filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:9905 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:9998 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:2054 filterByRange.AC on filterLabel.AC Allele Count (approx) filterByRange.afAfr on filterLimits.afAfr 0:1 filterLabel.afAfr AF African filterByRange.afEur on filterLimits.afEur 0:1 filterLabel.afEur AF European filterByRange.afEas on filterLimits.afEas 0:1 filterLabel.afEas AF East Asian skipEmptyFields on track han945Sv parent lrSv bigDataUrl /gbdb/$D/lrSv/han945.bb shortLabel Han 945 SVs longLabel Structural Variants from 945 Han Chinese (Long-read Sequencing) type bigBed 9 + itemRgb on visibility hide - mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC samples=$sampleCount + mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AF</b>: $alleleFreq<br><b>AC</b>: $AC<br><b>Samples</b>: $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 lrSv bigDataUrl /gbdb/$D/lrSv/tommoJp.bb shortLabel ToMMo 333 SVs longLabel Structural Variants from 333 Japanese Individuals (ToMMo, 111 Trios) type bigBed 9 + itemRgb on visibility hide - mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC + mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AF</b>: $alleleFreq<br><b>AC</b>: $AC filterValues.svType DEL,INS filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:99985 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:30649 filterByRange.insLen on filterLabel.insLen Insertion Length filter.alleleFreq 0:1 filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency filter.AC 0:444 filterByRange.AC on filterLabel.AC Allele Count track ga4kSv parent lrSv bigDataUrl /gbdb/$D/lrSv/ga4kSv.bb shortLabel GA4K 502 SVs longLabel Structural Variants from 502 Children's Mercy GA4K Probands (PacBio HiFi) type bigBed 9 + itemRgb on visibility hide - mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC~$AC AF=$alleleFreq carriers=$carrierCount/$sampleTotal + mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC (approx)</b>: $AC<br><b>AF</b>: $alleleFreq<br><b>Carriers</b>: $carrierCount/$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 lrSv bigDataUrl /gbdb/$D/lrSv/decodeSv.bb shortLabel deCODE 3622 SVs longLabel High-confidence Structural Variants from 3,622 Icelanders (deCODE, Oxford Nanopore) type bigBed 9 + itemRgb on visibility hide - mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen + mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen filterValues.svType DEL,INS,INSDEL filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:861080 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:22130 filterByRange.insLen on filterLabel.insLen Insertion Length skipEmptyFields on track hprc2v21Sv parent lrSv bigDataUrl /gbdb/$D/lrSv/hprc2v21.bb shortLabel HPRC v2.1 233 SVs longLabel Structural Variants from HPRC v2.1 Pangenome Graph (233 samples, minigraph-cactus) type bigBed 9 + itemRgb on visibility hide - mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC/$alleleNumber samples=$nSamples + mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AF</b>: $alleleFreq<br><b>AC</b>: $AC/$alleleNumber<br><b>Samples</b>: $nSamples filterValues.svType INS,DEL filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:99835 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:1064897 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:463 filterByRange.AC on filterLabel.AC Allele Count filter.alleleFreq 0:1 filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency filter.snarlLevel 0:7 filterByRange.snarlLevel on filterLabel.snarlLevel Snarl Level skipEmptyFields on # hprc2JasmineSv commented out: the Jasmine-merged HPRC v2 multi-caller # set is a test/comparison callset (the Hall lab is not happy with it) and # is not for release. bigBed, .as, converter and makeDoc are retained. # refs #36258 #track hprc2JasmineSv #parent lrSv #bigDataUrl /gbdb/$D/lrSv/hprc2Jasmine.bb #shortLabel HPRC2 Jasmine 231 SVs #longLabel Structural Variants from 231 HPRC v2 Assemblies (Jasmine merge of 14 SV callers) #type bigBed 9 + #itemRgb on #visibility dense #mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen samples=$nSamples/$alleleNumber AF=$alleleFreq callers=$nCallers ($callers) #filterValues.svType DEL,INS #filterType.svType multipleListOr #filterLabel.svType SV Type #filter.svLen 0:30176500 #filterByRange.svLen on #filterLabel.svLen SV Length #filter.insLen 0:30176500 #filterByRange.insLen on #filterLabel.insLen Insertion Length #filter.AC 0:231 #filterByRange.AC on #filterLabel.AC Carrier Sample Count #filter.alleleFreq 0:1 #filterByRange.alleleFreq on #filterLimits.alleleFreq 0:1 #filterLabel.alleleFreq Carrier Frequency #filter.nCallers 1:14 #filterByRange.nCallers on #filterLabel.nCallers Number of Supporting Callers #filterValues.callers DELLY,DeBreak,DeepVariant,PAV,SVDSS,SVIM,SVIM-asm,Sniffles2,cuteSV,cuteSV-asm,dipcall,longcallD,pbsv,sawfish #filterType.callers multipleListAnd #filterLabel.callers Supporting Callers #filterValues.sources PAV,dipcall,longcallD #filterType.sources multipleListAnd #filterLabel.sources Source Pipeline #skipEmptyFields on track hgsvc2Sv parent lrSv bigDataUrl /gbdb/$D/lrSv/hgsvc2.bb shortLabel HGSVC2 32 SVs longLabel Structural Variants from 32 Haplotype-Resolved Genomes (HGSVC2 freeze 4, Ebert 2021) type bigBed 9 + itemRgb on visibility hide - mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen samples=$sampleCount AC=$AC AF=$popAllAf + mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>Samples</b>: $sampleCount<br><b>AC</b>: $AC<br><b>AF</b>: $popAllAf filterValues.svType DEL,INS,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:57207414 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:108546 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 1:35 filterByRange.AC on filterLabel.AC Allele Count (carrier haplotypes) filter.sampleCount 1:35 filterByRange.sampleCount on filterLabel.sampleCount Sample Count filterValues.refTrf True,False filterType.refTrf multipleListOr filterLabel.refTrf In Tandem Repeat filter.refSd 0:1 filterByRange.refSd on filterLimits.refSd 0:1 filterLabel.refSd Segmental Duplication Overlap skipEmptyFields on track hgsvc3Sv parent lrSv bigDataUrl /gbdb/$D/lrSv/hgsvc3.bb shortLabel HGSVC3 65 SVs longLabel Structural Variants from 65 Diverse Samples (HGSVC3 ONT+HIFI) type bigBed 9 + itemRgb on visibility hide - mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen samples=$sampleCount AC=$AC + mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>Samples</b>: $sampleCount<br><b>AC</b>: $AC filterValues.svType DEL,INS,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:30176500 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:30176500 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 1:136 filterByRange.AC on filterLabel.AC Allele Count (carrier haplotypes) filter.sampleCount 1:65 filterByRange.sampleCount on filterLabel.sampleCount Sample Count filterValues.refTrf True,False filterType.refTrf multipleListOr filterLabel.refTrf In Tandem Repeat filter.refSd 0:1 filterByRange.refSd on filterLimits.refSd 0:1 filterLabel.refSd Segmental Duplication Overlap skipEmptyFields on # NOT FOR RELEASE: preliminary and unpublished (Kim et al. 2026 not out yet), # and the callset has breakend artifacts up to 190 Mb (e.g. a single "INV" # spanning all of chr4). Held on dev/alpha and kept out of the lrSvAll merge # (removed from databases.tsv) until the data is published and cleaned. track kwanhoSv parent lrSv bigDataUrl /gbdb/$D/lrSv/kwanho.bb shortLabel Kim PD 100 prelim longLabel Structural Variants from 100 Post-mortem Brains (Parkinson's disease, ILBD, Control; Kim et al. 2026, PacBio HiFi) - PRELIMINARY, data to be updated, contact the authors before using type bigBed 9 + itemRgb on visibility dense - mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC AF_PD=$afPd AF_HC=$afHc diff=$differentialRate + mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC</b>: $AC<br><b>AF (PD)</b>: $afPd<br><b>AF (HC)</b>: $afHc<br><b>Case-control diff</b>: $differentialRate filterValues.svType DEL,INS,DUP,INV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:200000000 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:20145 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:200 filterByRange.AC on filterLabel.AC Allele Count (PD+HC+ILBD) filter.qual 0:100 filterByRange.qual on filterLabel.qual Quality filter.afPd 0:1 filterByRange.afPd on filterLimits.afPd 0:1 filterLabel.afPd Allele Frequency (PD) filter.afHc 0:1 filterByRange.afHc on filterLimits.afHc 0:1 filterLabel.afHc Allele Frequency (HC) filter.afIlbd 0:1 filterByRange.afIlbd on filterLimits.afIlbd 0:1 filterLabel.afIlbd Allele Frequency (ILBD) filter.differentialRate -1:1 filterByRange.differentialRate on filterLimits.differentialRate -1:1 filterLabel.differentialRate Case-Control Differential (case - control) skipEmptyFields on track aprSv parent lrSv bigDataUrl /gbdb/$D/lrSv/apr.bb shortLabel Arab APR 53 SVs longLabel Structural Variants from the Arab Pangenome Reference (53 UAE-resident Arab samples) type bigBed 9 + itemRgb on visibility hide - mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC/$alleleNumber AF=$alleleFreq samples=$numSamples alts=$numAlts + mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC</b>: $AC/$alleleNumber<br><b>AF</b>: $alleleFreq<br><b>Samples</b>: $numSamples<br><b>Alts</b>: $numAlts filterValues.svType INS,DEL,CPX,MIXED filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:99885 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:584016 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:107 filterByRange.AC on filterLabel.AC Allele Count filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency skipEmptyFields on track cpc1Sv parent lrSv bigDataUrl /gbdb/$D/lrSv/cpc1.bb shortLabel CPC 58 SVs longLabel Structural Variants from the Chinese Pangenome Consortium (58 samples, CPC-only) type bigBed 9 + itemRgb on visibility hide - mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC/$alleleNumber AF=$alleleFreq samples=$numSamples alts=$numAlts + mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC</b>: $AC/$alleleNumber<br><b>AF</b>: $alleleFreq<br><b>Samples</b>: $numSamples<br><b>Alts</b>: $numAlts filterValues.svType INS,DEL,CPX,MIXED filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:8998096 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:376583 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:116 filterByRange.AC on filterLabel.AC Allele Count filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency skipEmptyFields on track chirmade101Sv parent lrSv bigDataUrl /gbdb/$D/lrSv/chirmade101.bb shortLabel SVatalog 101 SVs longLabel Structural Variants from 101 Long-read WGS (GWAS SVatalog, Chirmade 2026) type bigBed 9 + itemRgb on visibility hide - mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen genes=$geneCount + mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>Genes</b>: $geneCount filterValues.svType DEL,INS,DUP,INV,CPX filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:1321484 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:31711 filterByRange.insLen on filterLabel.insLen Insertion Length filter.geneCount 0:200 filterByRange.geneCount on filterLabel.geneCount Gene Count skipEmptyFields on # NOT FOR RELEASE: data received from Eichler lab via email, not yet published. # Do not add to lrSvAll merged track until a preprint or paper is available. track lrSv1kLin parent lrSv bigDataUrl /gbdb/$D/lrSv/lin1218.bb shortLabel 1KG Linear 1218 SVs longLabel Structural Variants from 1,218 Individuals (1000 Genomes, Linear Long-read) type bigBed 9 + itemRgb on visibility hide - mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC/$AN AF=$AF AF_AFR=$afAfr AF_EUR=$afEur samples=$NS + mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC</b>: $AC/$AN<br><b>AF</b>: $AF<br><b>AF (African)</b>: $afAfr<br><b>AF (European)</b>: $afEur<br><b>Samples</b>: $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 filterLabel.AC Allele Count filter.AF 0:1 filterByRange.AF on filterLimits.AF 0:1 filterLabel.AF Allele Frequency filterByRange.afAfr on filterLimits.afAfr 0:1 filterLabel.afAfr AF African filterByRange.afAmr on filterLimits.afAmr 0:1 filterLabel.afAmr AF Admixed American filterByRange.afEas on filterLimits.afEas 0:1 filterLabel.afEas AF East Asian filterByRange.afEur on filterLimits.afEur 0:1 filterLabel.afEur AF European 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