00e086afbcb8296c6aef946c13eeb777f34bac02 max Mon May 11 07:03:10 2026 -0700 mei: new track for HGSVC3 mobile element insertions on hg38 and hs1 12,642 MEIs on hg38, 12,919 on hs1, from the HGSVC3 callset (Logsdon et al. 2025). Single shared trackDb stanza in human/mei.ra with $D substitution. Okabe-Ito colors, INS-svLen:carrierCount item names, inserted DNA in an insertSeq field. Cross-link to lrSv via relatedTracks.ra. refs #37524 diff --git src/hg/makeDb/trackDb/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra index 2d717891115..ec59d8759e6 100644 --- src/hg/makeDb/trackDb/relatedTracks.ra +++ src/hg/makeDb/trackDb/relatedTracks.ra @@ -91,30 +91,34 @@ # mm10 ENCODE4 Regulation: mm10 encode4Reg encode3Reg Previous ENCODE3 Regulation track mm10 encode3Reg encode4Reg New ENCODE4 Regulation track mm10 encode4Reg cCREs Related ENCODE4 cCRE annotations mm10 cCREs encode4Reg Related ENCODE4 regulation data # hg38 long-read SV supertrack cross-links to other SV resources: hg38 lrSv gnomadStructuralVariants Short-read structural variants from gnomAD v4.1 hg38 gnomadStructuralVariants lrSv Long-read structural variants across multiple cohorts hg38 lrSv dbVarSv NCBI dbVar structural variants (short-read and long-read, germline and clinical) hg38 dbVarSv lrSv Long-read structural variants across multiple cohorts hg38 lrSv dgvPlus Database of Genomic Variants (DGV) structural variation catalog hg38 dgvPlus lrSv Long-read structural variants across multiple cohorts hg38 lrSv giabSv Genome in a Bottle high-confidence SV benchmark callsets hg38 giabSv lrSv Long-read structural variants across multiple cohorts +hg38 lrSv mei Polymorphic Mobile Element Insertions (Alu, L1, SVA, HERVK, snRNA) from HGSVC3 long-read assemblies +hg38 mei lrSv Long-read structural variants across multiple cohorts (parent SV callsets for the HGSVC3 MEI track) +hs1 lrSv mei Polymorphic Mobile Element Insertions (Alu, L1, SVA, HERVK, snRNA) from HGSVC3 long-read assemblies +hs1 mei lrSv Long-read structural variants across multiple cohorts (parent SV callsets for the HGSVC3 MEI track) # PrimateAI-3D cross-links: hg38 primateAi alphaMissense AlphaMissense, a similar deep-learning missense pathogenicity predictor hg38 alphaMissense primateAi PrimateAI-3D, a similar deep-learning missense pathogenicity predictor using primate variation hg38 primateAi revel REVEL, an ensemble missense pathogenicity score built from multiple predictors hg38 revel primateAi PrimateAI-3D, a missense pathogenicity predictor using primate variation and 3D protein structure hg19 primateAi revel REVEL, an ensemble missense pathogenicity score built from multiple predictors hg19 revel primateAi PrimateAI-3D, a missense pathogenicity predictor using primate variation and 3D protein structure # ClinPred cross-links: hg38 clinPred revel REVEL, an ensemble missense pathogenicity score using a similar machine-learning approach hg38 revel clinPred ClinPred, an ensemble missense pathogenicity predictor that incorporates gnomAD allele frequency hg38 clinPred caddSuper CADD, a similar deleteriousness score hg38 caddSuper clinPred ClinPred, a missense-only pathogenicity predictor