4f8f8773bec66a9e993e9897e0b032c6e97dead8 max Fri May 15 10:12:29 2026 -0700 mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524 diff --git src/hg/makeDb/trackDb/human/mei.ra src/hg/makeDb/trackDb/human/mei.ra index d2f49d01eee..bfe5d2431c3 100644 --- src/hg/makeDb/trackDb/human/mei.ra +++ src/hg/makeDb/trackDb/human/mei.ra @@ -52,15 +52,119 @@ longLabel Mobile Element Insertions in 3,202 1000 Genomes Samples (DeepMEI) type bigBed 9 + itemRgb on visibility pack mouseOver <b>${teClass}</b> insertion<br>Carriers: ${carrierCount}/${sampleCount} samples<br>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) + type bigBed 9 + + itemRgb on + visibility pack + mouseOver <b>${teClass}</b> insertion (${svLen} bp)<br>Carrier haplotypes: ${altAlleleCount}/${alleleNumber}<br>Allele frequency: ${altAlleleFreq}<br>NyuWa AF: ${nyuwaAF}, 1KGP AF: ${kgpAF}<br>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: 8,988 curated L1-HS Insertion Polymorphisms (Mir 2015, lifted from hg19) + type bigBed 9 + + itemRgb on + visibility pack + mouseOver <b>${name}</b><br>Lineage: ${lineage}<br>Sub-group: ${subGroups}<br>Integrity: ${integrity}<br>Pseudo-AF: ${pseudoAlleleFreq}<br>SRIPs: ${sripCount} from ${sampleCount} samples in ${studyCount} studies<br>Gene: ${gene} + filter.pseudoAlleleFreq 0:1 + filterByRange.pseudoAlleleFreq on + filterLimits.pseudoAlleleFreq 0:1 + filterLabel.pseudoAlleleFreq Pseudo-allele frequency + filter.sripCount 0:1000 + filterByRange.sripCount on + filterLabel.sripCount SRIP count (sample observations) + filter.studyCount 0:30 + filterByRange.studyCount on + filterLabel.studyCount Study count + filterValues.lineage germline,somatic,germline\,somatic,unknown + filterType.lineage multipleListOr + filterLabel.lineage Lineage + filterValues.pcrValidated yes,no + filterType.pcrValidated multipleListOr + filterLabel.pcrValidated PCR validated + filterValues.inReferenceL1HS yes,no + filterType.inReferenceL1HS multipleListOr + filterLabel.inReferenceL1HS In reference L1HS + skipEmptyFields on + + track meiEul1dbRef + parent mei + bigDataUrl /gbdb/$D/mei/eul1dbRef.bb + shortLabel euL1db Ref L1HS + longLabel euL1db: 1,540 L1-HS Copies Present in the Reference Genome (lifted from hg19) + type bigBed 9 + + itemRgb on + visibility hide + mouseOver <b>${subGroup}</b><br>Integrity: ${integrity}<br>L1HS consensus: ${refStart}-${refStop}<br>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) + type bigBed 9 + + itemRgb on + visibility pack + tableBrowser off + mouseOver <b>${teClass}</b> insertion (${svLen} bp, ${meiSubfamily})<br>Allele count: ${altAlleleCount} of ~2000<br>Allele frequency: ${altAlleleFreq}<br>MELT ASSESS: ${assess}/5<br>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