8e55bcac3b1cf604a3cebbb7eaf4aac109449f76 max Tue Sep 22 06:13:02 2026 -0700 changing track name, refs #37524 diff --git src/hg/makeDb/trackDb/human/mei.ra src/hg/makeDb/trackDb/human/mei.ra index 1bdaecd748c..5dac8b2b181 100644 --- src/hg/makeDb/trackDb/human/mei.ra +++ src/hg/makeDb/trackDb/human/mei.ra @@ -1,176 +1,176 @@ track mei superTrack on -shortLabel Mobile Insertions -longLabel Mobile element insertions (polymorphic) +shortLabel Mobile Element Insertions +longLabel Mobile Element Insertions (polymorphic) group varRep visibility hide track meiHgsvc3 parent mei bigDataUrl /gbdb/$D/mei/hgsvc3.bb shortLabel HGSVC3 65 MEIs longLabel Mobile element insertions in 65 HGSVC3 long-read assembled samples dataVersion HGSVC3 Mobile Elements release 1.0, 2024-12-11 type bigBed 9 + itemRgb on visibility pack mouseOver ${teClass} insertion (${svLen} bp)
Carriers: ${carrierCount}/${sampleCount} samples
Allele frequency: ${altAlleleFreq}
Callers: ${callerCount}/2 (PALMER ${palmer}, L1ME-AID ${l1meAid}) filterValues.teClass Alu,L1,SVA,HERVK,snRNA filterType.teClass multipleListOr filterLabel.teClass Mobile Element Class filter.svLen 0:9478 filterByRange.svLen on filterLabel.svLen Insertion Length (bp) filter.altAlleleFreq 0:1 filterByRange.altAlleleFreq on filterLimits.altAlleleFreq 0:1 filterLabel.altAlleleFreq Allele Frequency filter.carrierCount 0:65 filterByRange.carrierCount on filterLabel.carrierCount Carrier Sample Count filterValues.callerCount 1,2 filterType.callerCount multipleListOr filterLabel.callerCount Caller Count (1=single, 2=both) filterValues.l1meAid Yes,No filterType.l1meAid multipleListOr filterLabel.l1meAid L1ME-AID Validated filterValues.palmer Yes,No filterType.palmer multipleListOr filterLabel.palmer PALMER Validated filterValues.refTrf True,False filterType.refTrf multipleListOr filterLabel.refTrf In Tandem Repeat filter.refSegDup 0:1 filterByRange.refSegDup on filterLimits.refSegDup 0:1 filterLabel.refSegDup Segmental Duplication Overlap skipEmptyFields on track meiDeepmei1kg parent mei bigDataUrl /gbdb/$D/mei/deepmei1kg.bb shortLabel DeepMEI 1000G MEIs longLabel Mobile element insertions in 3,202 1000 Genomes samples (DeepMEI) dataVersion DeepMEI 1000 Genomes high-confidence callset, 2022-11-21 type bigBed 9 + itemRgb on visibility pack mouseOver ${teClass} insertion
Carriers: ${carrierCount}/${sampleCount} samples
Allele frequency: ${altAlleleFreq} filterValues.teClass Alu,L1,SVA filterType.teClass multipleListOr filterLabel.teClass Mobile Element Class filter.altAlleleFreq 0:1 filterByRange.altAlleleFreq on filterLimits.altAlleleFreq 0:1 filterLabel.altAlleleFreq Allele Frequency filter.carrierCount 0:3202 filterByRange.carrierCount on filterLabel.carrierCount Carrier Sample Count track meiHmeid parent mei bigDataUrl /gbdb/$D/mei/hmeid.bb shortLabel HMEID 5675 MEIs longLabel Mobile element insertions in 5,675 NyuWa + 1000 Genomes samples (HMEID v1.1) dataVersion HMEID v1.1 type bigBed 9 + itemRgb on visibility pack mouseOver ${teClass} insertion (${svLen} bp)
Carrier haplotypes: ${altAlleleCount}/${alleleNumber}
Allele frequency: ${altAlleleFreq}
NyuWa AF: ${nyuwaAF}, 1KGP AF: ${kgpAF}
MELT ASSESS: ${assess}/5 filterValues.teClass Alu,L1,SVA,HERVK filterType.teClass multipleListOr filterLabel.teClass Mobile Element Class filter.svLen -1:8757 filterByRange.svLen on filterLabel.svLen Insertion Length (bp, -1 if unknown) filter.altAlleleFreq 0:1 filterByRange.altAlleleFreq on filterLimits.altAlleleFreq 0:1 filterLabel.altAlleleFreq Allele Frequency (all) filter.nyuwaAF 0:1 filterByRange.nyuwaAF on filterLimits.nyuwaAF 0:1 filterLabel.nyuwaAF NyuWa Allele Frequency filter.kgpAF 0:1 filterByRange.kgpAF on filterLimits.kgpAF 0:1 filterLabel.kgpAF 1KGP Allele Frequency filterValues.assess 3,4,5 filterType.assess multipleListOr filterLabel.assess MELT ASSESS Score track meiEul1db parent mei bigDataUrl /gbdb/$D/mei/eul1db.bb shortLabel euL1db Insertions longLabel euL1db: curated L1-HS insertion polymorphisms (Mir 2015) dataVersion euL1db v1.00, 2014-10-14 type bigBed 9 + itemRgb on visibility pack mouseOver ${name}
Lineage: ${lineage}
Sub-group: ${subGroups}
Integrity: ${integrity}
Pseudo-AF: ${pseudoAlleleFreq}
SRIPs: ${sripCount} from ${sampleCount} samples in ${studyCount} studies
Gene: ${gene} filter.pseudoAlleleFreq 0:1 filterByRange.pseudoAlleleFreq on filterLimits.pseudoAlleleFreq 0:1 filterLabel.pseudoAlleleFreq Pseudo-allele frequency filter.sripCount 0:675 filterByRange.sripCount on filterLabel.sripCount SRIP count (sample observations) filter.studyCount 0:10 filterByRange.studyCount on filterLabel.studyCount Study count filterValues.lineage germline,somatic,germline\,somatic,unknown filterType.lineage multipleListOr filterLabel.lineage Lineage filterValues.pcrValidated yes,no filterType.pcrValidated multipleListOr filterLabel.pcrValidated PCR validated filterValues.inReferenceL1HS yes,no filterType.inReferenceL1HS multipleListOr filterLabel.inReferenceL1HS In reference L1HS skipEmptyFields on track meiEul1dbRef parent mei bigDataUrl /gbdb/$D/mei/eul1dbRef.bb shortLabel euL1db Ref L1HS longLabel euL1db: L1-HS copies present in the reference genome (Mir 2015) dataVersion euL1db v1.00, 2014-10-14 type bigBed 9 + itemRgb on visibility hide mouseOver ${subGroup}
Integrity: ${integrity}
L1HS consensus: ${refStart}-${refStop}
Length: ${elementLen} bp filterValues.subGroup L1HS-Ta,L1HS-PreTa,L1HS-undef filterType.subGroup multipleListOr filterLabel.subGroup L1HS sub-group filterValues.integrity full-length,5prime-truncated,3prime-truncated,internal_fragment filterType.integrity multipleListOr filterLabel.integrity Integrity track meiSwegen parent mei bigDataUrl /gbdb/$D/mei/_swegen.bb shortLabel SweGen 1000 MEIs longLabel Mobile element insertions in 1,000 SweGen Swedish samples (MELT, lifted from GRCh37) dataVersion SweGen MELT callset, 2018-03-14 type bigBed 9 + itemRgb on visibility pack tableBrowser off mouseOver ${teClass} insertion (${svLen} bp, ${meiSubfamily})
Allele count: ${altAlleleCount} of ~2000
Allele frequency: ${altAlleleFreq}
MELT ASSESS: ${assess}/5
FILTER: ${filterStatus} filterValues.teClass Alu,L1,SVA,HERVK filterType.teClass multipleListOr filterLabel.teClass Mobile Element Class filter.svLen -1:8757 filterByRange.svLen on filterLabel.svLen Insertion Length (bp, -1 if unknown) filter.altAlleleFreq 0:1 filterByRange.altAlleleFreq on filterLimits.altAlleleFreq 0:1 filterLabel.altAlleleFreq Allele Frequency filterValues.assess 0,1,2,3,4,5 filterType.assess multipleListOr filterLabel.assess MELT ASSESS Score filterValues.filterStatus PASS,hDP,rSD,s25 filterType.filterStatus multipleListOr filterLabel.filterStatus MELT FILTER Status