# GENERATE FILE DO NOT EDIT # common to H9 haplotypes (common_h9.trackDb.txt) track cytoBandIdeo shortLabel Ideogram longLabel Ideogram group map visibility dense type bigBed 4 + bigDataUrl ideoGram/ideoGram.bb track Flagger shortLabel Flagger longLabel Flagger group annotations type bigBed 9 itemRgb on visibility hide bigDataUrl flagger/final_flagger_prediction_hap2.bb html ../html/empty.html group map track PacBio_HiFi bigDataUrl t2t_h9_hifi/t2t_h9_v01_hap2.t2t_h9_hifi.bam shortLabel PacBio_HiFi longLabel PacBio_HiFi html ../html/empty.html type bam group map track ONT_2023 bigDataUrl h9_ont_2023/t2t_h9_v01_hap2.h9_ont_2023.bam shortLabel ONT_2023 longLabel ONT_2023 html ../html/empty.html type bam group map track ONT_2024 bigDataUrl h9_ont_2024/t2t_h9_v01_hap2.h9_ont_2024.bam shortLabel ONT_2024 longLabel ONT_2024 html ../html/empty.html type bam group map track repeatMasker shortLabel Repeat Masker longLabel Repeat Masker type bigRmsk 9 + group rep visibility hide bigDataUrl repeatMasker/t2t_h9_v01_hap2.sorted.fa.out.bb xrefDataUrl repeatMasker/t2t_h9_v01_hap2.fa.align.bb html ../html/empty.html track simpleRepeat shortLabel Simple repeats longLabel Simple repeats type bigBed 4 + group rep visibility hide bigDataUrl simpleRepeat/simpleRepeat.bb html ../html/empty.html track windowMasker shortLabel Window Masker longLabel Window Masker labelFields name defaultLabelFields none type bigBed 4 group rep visibility hide bigDataUrl windowMasker/t2t_h9_v01_hap2.windowmasker.bb html ../html/empty.html track sedefSegDupsSuper superTrack on hide shortLabel Segmental Duplications longLabel SEDEF Segmental Duplications group rep track sedefSegDups parent sedefSegDupsSuper shortLabel Segmental Duplications longLabel SEDEF Segmental Duplications group rep type bigBed 9 + visibility hide itemRgb on labelFields name defaultLabelFields name priority 1 bigDataUrl sedef/t2t_h9_v01_hap2.sedef.bb url /cgi-bin/hgTracks?genome=$D&position=$:$-$ urlLabel Source locus link html ../html/sedefSegDups.html filter.fracMatch 0.0 filterLabel.fracMatch Minimum fraction identity filter.size 0 filterLabel.size Minimum genomic coverage in bases filter.span 0 filterLabel.span Minimum genomic span in bases track sedefSegDupsAnalysis parent sedefSegDupsSuper shortLabel SEDEF Seg Dups PSLs longLabel SEDEF Segmental Duplications Analysis PSLs bigDataUrl sedef/t2t_h9_v01_hap2.sedef.analysis.bb group rep html ../html/empty.html type bigPsl color 128,92,10 canPack on searchIndex name visibility hide labelFields name defaultLabelFields name baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 priority 2 track HumAS_HMMER superTrack on hide shortLabel Human AS-HOR longLabel Human Alpha Satellite Higher-Order Repeats type bigBed 9 group map visibility hide track AS_HOR_SF parent HumAS_HMMER shortLabel AS-HOR+SF longLabel HMMER AS-HOR+SF type bigBed 9 group map visibility dense bigDataUrl AS-HOR/AS-HOR+SF-vs-t2t_h9_v01_hap2.bb html ../html/empty.html filterLabel.name AS/HOR/SF name filterText.name * filterType.name wildcard track AS_HOR parent HumAS_HMMER shortLabel AS-HOR longLabel HMMER AS-HOR type bigBed 9 group map visibility dense bigDataUrl AS-HOR/AS-HOR-vs-t2t_h9_v01_hap2.bb html ../html/empty.html filterLabel.name AS/HOR name filterText.name * filterType.name wildcard track AS_SF parent HumAS_HMMER shortLabel AS-SF longLabel HMMER AS-SF type bigBed 9 group map visibility dense bigDataUrl AS-HOR/AS-SF-vs-t2t_h9_v01_hap2.bb html ../html/empty.html filterLabel.name AS/SF name filterText.name * filterType.name wildcard track AS_strand parent HumAS_HMMER shortLabel AS-strand longLabel HMMER AS-strand type bigBed 9 group map visibility dense bigDataUrl AS-HOR/AS-strand-vs-t2t_h9_v01_hap2.bb html ../html/empty.html filterLabel.name AS name filterText.name * filterType.name wildcard track snp_density shortLabel SNP density longLabel SNP density hap1 logo on type bigWig viewLimits 0:0.07 color 92,126,255 group rep visibility hide bigDataUrl snp-density/t2t_h9_v01_hap2.hap1.snpdensity.bw html ../html/empty.html track encode_isoseq type bam bigDataUrl encode-lrRNA/ENCSR044ARQ.bam shortLabel ENCODE IsoSeq longLabel ENCODE IsoSeq html ../html/empty.html visibility hide group rna track modkit_methyl type bigMethyl bigDataUrl modkit/t2t_h9_v01_hap2_clean.bb shortLabel ModKit methylation (dip) longLabel ModKit methylation (diploid mapping) html ../html/empty.html visibility hide group regulation track modkit_methyl_wig type bigWig bigDataUrl modkit/t2t_h9_v01_hap2_clean.bw shortLabel ModKit methylation wiggle (dip) longLabel ModKit methylation wiggle (diploid mapping) html ../html/empty.html visibility hide group regulation track encode_h9_miRNA_seq bigDataUrl encode-h9-miRNA-seq/encode-h9-miRNA-seq.bam shortLabel H9 miRNA-Seq longLabel ENCODE H9 miRNA-Seq html ../html/empty.html type bam group miRNA track NCGM_brain_DRP010077 bigDataUrl lrRNA/NCGM-brain-DRP010077/t2t_h9_v01_hap2.NCGM-brain-DRP010077.bam shortLabel NCGM Brain IsoSeq longLabel NCGM Brain IsoSeq html ../html/empty.html type bam group rna track cat_consensusV2 shortLabel CAT Genes V2 longLabel CAT Consensus Gene Set V2 type bigGenePred bigDataUrl cat-genesV2/consensus/t2t_h9_v01_hap2.cat-genes.ranks.bb visibility hide group genes itemRgb on searchIndex name,name2,gene_id,transcript_id,source_transcript,original_gene_id labelFields name,name2,gene_id,transcript_id,source_transcript,original_gene_id defaultLabelFields name2 labelSeparator "/" html ../html/empty.html priority 1.0 filterLabel.name2 Gene symbol filterType.name2 wildcard filterText.name2 * filterLabel.transcript_rank Gene transcript rank filterByRange.transcript_rank on filter.transcript_rank 0:1000 track cat_notch2nl_region_genesV2 shortLabel NOTCH2NL Region Genes V2 longLabel CAT NOTCH2NL Region Genes V2 type bigGenePred bigDataUrl cat-genesV2/consensus/t2t_h9_v01_hap2.cat-genes.ranks.NOTCH2NL-region.bb labelSeparator "/" visibility hide group genes itemRgb on searchIndex name,name2,gene_id,transcript_id,source_transcript,original_gene_id labelFields name,name2,gene_id,transcript_id,source_transcript,original_gene_id defaultLabelFields name2 labelSeparator "/" html ../html/empty.html priority 1.1 filterLabel.name2 Gene symbol filterType.name2 wildcard filterText.name2 * filterLabel.transcript_rank Gene transcript rank filterByRange.transcript_rank on filter.transcript_rank 0:1000 track cat_notch2nl_genesV2 shortLabel NOTCH2NL Genes V2 longLabel CAT NOTCH2NL V2 type bigGenePred bigDataUrl cat-genesV2/consensus/t2t_h9_v01_hap2.cat-genes.ranks.NOTCH2NL.bb visibility hide group genes itemRgb on searchIndex name,name2,gene_id,transcript_id,source_transcript,original_gene_id labelFields name,name2,gene_id,transcript_id,source_transcript,original_gene_id defaultLabelFields name2 labelSeparator "/" html ../html/empty.html priority 1.2 filterLabel.name2 Gene symbol filterType.name2 wildcard filterText.name2 * filterLabel.transcript_rank Gene transcript rank filterByRange.transcript_rank on filter.transcript_rank 0:1000 track gencodeV48_orthlogs shortLabel GENCODE V48_Orthlogs longLabel GENCODE V48_Orthlogs type bigGenePred bigDataUrl gencodeV48-orthlogos/t2t_h9_v01_hap2.gencodeV48-map.bb visibility hide group genes itemRgb on searchIndex name,name2 labelFields name,name2 defaultLabelFields name2 labelSeparator "/" html ../html/empty.html track centeny shortLabel CENP-B boxes longLabel CENP-B box annotations type bigBed 9 itemRgb on group hsCompGeno visibility hide bigDataUrl centeny/centeny-hap2-hap1.bb html ../html/empty.html url /cgi-bin/hgTracks?genome=t2t_h9_v01_hap1&position=$$ urlLabel t2t_h9_v01_hap1: mouseOver t2t_h9_v01_hap1: ${name} labelFields name defaultLabelFields name priority 20 track atac_seq_peaks superTrack on hide shortLabel ATAC-Seq peaks longLabel ATAC-Seq peaks type bigBed 5 + group regulation color 128,0,0 visibility hide track atac_seq_peaks_specific parent atac_seq_peaks shortLabel ATAC-Seq specific peaks longLabel ATAC-Seq specific peaks type bigBed 5 + group regulation visibility pack bigDataUrl atac-seq-peaks/atac-seq_H9_q20_hap2_specific_peaks.bb html ../html/empty.html priority 1 track atac_seq_peaks_enriched parent atac_seq_peaks shortLabel ATAC-Seq enriched peaks longLabel ATAC-Seq enriched peaks type bigBed 5 + group regulation visibility pack bigDataUrl atac-seq-peaks/atac-seq_H9_q20_hap2_enriched_peaks.bb html ../html/empty.html priority 2 track dna_brnn shortLabel DNA-BRNN longLabel DNA-BRNN type bigBed 3 group map color 0,128,0 visibility hide bigDataUrl dna-brnn/H9v0.1.hap2.three.hapchr.bb html ../html/empty.html priority 40 track chm13_variants shortLabel CHM13 variants longLabel CHM13 variants bigDataUrl variants/H9_hap2_linear.g.chrhap.vcf.gz type vcfTabix visibility hide group phenDis html ../html/empty.html priority 10 track centros-telos shortLabel centromeres & telomeres longLabel centromeres & telomeres type bigBed 4 group map visibility hide bigDataUrl centros-telos/t2t_h9_v01_hap2.centros-telos.bb html ../html/empty.html track teloscope shortLabel Teloscope longLabel Teloscope v1.3 type bigBed 4 group map visibility hide bigDataUrl teloscope/t2t_h9_v01_hap2.teloscope.bb html ../html/empty.html track hi_c_ab_10kb shortLabel Hi-C A/B 10kb longLabel Hi-C A/B 10kb resolution type bigWig viewLimits -2.0:2.0 color 92,155,26 group regulation visibility hide bigDataUrl Hi-C-AB/H9_T2T_v0.1_collated.10000.AB.flipped.bw html ../html/empty.html track hi_c_ab_100kb shortLabel Hi-C A/B 100kb longLabel Hi-C A/B 100kb resolution type bigWig viewLimits -2.0:2.0 color 92,155,26 group regulation visibility hide bigDataUrl Hi-C-AB/H9_T2T_v0.1_collated.100000.AB.flipped.bw html ../html/empty.html # intentionally left blank (common_h9.trackDb.txt) # common to H9 and CHM13 assemblies (common_h9_hs1.trackDb.txt) track mirGeneDb_blast shortLabel mirGeneDb BLAST longLabel mirGeneDb BLAST bigDataUrl miRNA-blast/t2t_h9_v01_hap2.mirGeneDb.bb group miRNA html ../html/empty.html type bigPsl priority 10.1 color 0,100,120 canPack on searchIndex name visibility hide baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 track tRNAs shortLabel tRNAs longLabel tRNAscan-SE tRNA annotations group genes visibility hide itemRgb on type bigBed 12 + bigDataUrl tRNA/tRNA.bb html ../html/tRNAs.html # sedefSegDupsFiltSuper track sedef_t2t_h9_v01_hap2_98 parent sedefSegDupsFiltSuper shortLabel Sedef t2t_h9_v01_hap2 98% longLabel Sedef t2t_h9_v01_hap2 98% bigDataUrl sedef-venn/asm/t2t_h9_v01_hap2.sedef.0.98.bb group rep html ../html/empty.html type bigBed 12 color 128,10,92 canPack on visibility hide priority 10 track sedef_t2t_h9_v01_hap2_90 parent sedefSegDupsFiltSuper shortLabel Sedef t2t_h9_v01_hap2 90% longLabel Sedef t2t_h9_v01_hap2 90% bigDataUrl sedef-venn/asm/t2t_h9_v01_hap2.sedef.0.90.bb group rep html ../html/empty.html type bigBed 12 color 128,10,92 canPack on visibility hide priority 11 # intentionally left blank (common_h9_hs1.trackDb.txt) # common template for H9, hs1, and hg38 (common_h9_hs1_hg38.trackDb.txt) track mirna_pre100pct type bigPsl shortLabel pre-miRNA 100% longLabel precursor-miRNA 100% group miRNA visibility hide bigDataUrl miRNA-ortho/t2t_h9_v01_hap2.mirbase.mirpre.blastn.100pct.matmir.filtered.bb color 150,0,32 canPack on baseColorUseSequence lfExtra baseColorDrawOpt diffBases indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 searchIndex name html ../html/empty.html track mirna_pre9095pct type bigPsl shortLabel pre-miRNA 90% longLabel precursor-miRNA 90%, 95% cover group miRNA visibility hide bigDataUrl miRNA-ortho/t2t_h9_v01_hap2.mirbase.mirpre.blastn.9095pct.matmir.filtered.bb html ../html/empty.html color 150,0,32 canPack on baseColorUseSequence lfExtra baseColorDrawOpt diffBases indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 searchIndex name track goh_2025 shortLabel Goh 2025 neurodev CNVs longLabel Goh 2025 neurodevelopment CNVs bigDataUrl goh-2025/goh-2025.bb group phenDis html ../html/goh-2025.html type bigPsl priority 20.1 color 0,100,120 canPack on searchIndex name visibility hide baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 priority 20 mouseOver ${name} (${strand}) # intentionally left blank (common_h9_hs1_hg38.trackDb.txt) # common to H9, CHM13, hg38, and hg19 assemblies (common_h9_hs1_hg38_hg19.trackDb.txt) track notch2nl-uniq-genes shortLabel NOTCH2NL Unique Genes longLabel NOTCH2NL Region Unique Genes type bigBed 4 color 48,25,52 group genes visibility hide bigDataUrl notch2nl/uniq-gene.t2t_h9_v01_hap2.bb html ../html/notch2nl-uniq-genes.html # intentionally left blank (common_h9_hs1_hg38_hg19.trackDb.txt) # common to H9, CHM13, and hg19 assemblies (common_h9_hs1_hg19.trackDb.txt) track assou_2020 shortLabel Assou 2020 pluripotent abnormalities longLabel Assou 2020 pluripotent abnormalities bigDataUrl assou-2020/assou-2020.bb group phenDis html ../html/assou-2020.html type bigPsl priority 20.1 color 0,100,120 canPack on searchIndex name visibility hide baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 priority 20 # intentionally left blank (common_h9_hs1_hg19.trackDb.txt) # super track for genomic alignments (common_genomic_aln_super.trackDb.txt) track hg38_genomic_aln_super superTrack on hide shortLabel hg38 alignments longLabel hg38 alignments group hsCompGeno # intentionally left blank (common_genomic_aln_super.trackDb.txt) # super track for genomic alignments (common_genomic_aln_super.trackDb.txt) track hs1_genomic_aln_super superTrack on hide shortLabel hs1 alignments longLabel hs1 alignments group hsCompGeno # intentionally left blank (common_genomic_aln_super.trackDb.txt) # super track for genomic alignments (common_genomic_aln_super.trackDb.txt) track t2t_h9_v01_hap1_genomic_aln_super superTrack on hide shortLabel t2t_h9_v01_hap1 alignments longLabel t2t_h9_v01_hap1 alignments group hsCompGeno # intentionally left blank (common_genomic_aln_super.trackDb.txt) 1# minimap2 genomic alignments (common_mm2_genomic_aln.trackDb.txt) # needs common_genomic_aln_super.trackDb.txt included ones track hs1_minimap_chain parent hs1_genomic_aln_super type bigChain hs1 shortLabel hs1 mm2 chain longLabel hs1 minimap2 chain bigDataUrl mm2-genomic-aln/hs1/t2t_h9_v01_hap2.hs1.chain.bb linkDataUrl mm2-genomic-aln/hs1/t2t_h9_v01_hap2.hs1.link.bb visibility hide html ../html/empty.html group hsCompGeno priority 10 track hs1_minimap_syn_chain parent hs1_genomic_aln_super type bigChain hs1 shortLabel hs1 syn mm2 chain longLabel hs1 syntenic minimap2 chain bigDataUrl mm2-genomic-aln/hs1/t2t_h9_v01_hap2.hs1.syn.chain.bb linkDataUrl mm2-genomic-aln/hs1/t2t_h9_v01_hap2.hs1.syn.link.bb visibility hide html ../html/empty.html group hsCompGeno priority 11 # intentionally left blank (common_mm2_genomic_aln.trackDb.txt) 1# minimap2 genomic alignments (common_mm2_genomic_aln.trackDb.txt) # needs common_genomic_aln_super.trackDb.txt included ones track hg38_minimap_chain parent hg38_genomic_aln_super type bigChain hg38 shortLabel hg38 mm2 chain longLabel hg38 minimap2 chain bigDataUrl mm2-genomic-aln/hg38/t2t_h9_v01_hap2.hg38.chain.bb linkDataUrl mm2-genomic-aln/hg38/t2t_h9_v01_hap2.hg38.link.bb visibility hide html ../html/empty.html group hsCompGeno priority 10 track hg38_minimap_syn_chain parent hg38_genomic_aln_super type bigChain hg38 shortLabel hg38 syn mm2 chain longLabel hg38 syntenic minimap2 chain bigDataUrl mm2-genomic-aln/hg38/t2t_h9_v01_hap2.hg38.syn.chain.bb linkDataUrl mm2-genomic-aln/hg38/t2t_h9_v01_hap2.hg38.syn.link.bb visibility hide html ../html/empty.html group hsCompGeno priority 11 # intentionally left blank (common_mm2_genomic_aln.trackDb.txt) 1# minimap2 genomic alignments (common_mm2_genomic_aln.trackDb.txt) # needs common_genomic_aln_super.trackDb.txt included ones track t2t_h9_v01_hap1_minimap_chain parent t2t_h9_v01_hap1_genomic_aln_super type bigChain t2t_h9_v01_hap1 shortLabel t2t_h9_v01_hap1 mm2 chain longLabel t2t_h9_v01_hap1 minimap2 chain bigDataUrl mm2-genomic-aln/t2t_h9_v01_hap1/t2t_h9_v01_hap2.t2t_h9_v01_hap1.chain.bb linkDataUrl mm2-genomic-aln/t2t_h9_v01_hap1/t2t_h9_v01_hap2.t2t_h9_v01_hap1.link.bb visibility hide html ../html/empty.html group hsCompGeno priority 10 track t2t_h9_v01_hap1_minimap_syn_chain parent t2t_h9_v01_hap1_genomic_aln_super type bigChain t2t_h9_v01_hap1 shortLabel t2t_h9_v01_hap1 syn mm2 chain longLabel t2t_h9_v01_hap1 syntenic minimap2 chain bigDataUrl mm2-genomic-aln/t2t_h9_v01_hap1/t2t_h9_v01_hap2.t2t_h9_v01_hap1.syn.chain.bb linkDataUrl mm2-genomic-aln/t2t_h9_v01_hap1/t2t_h9_v01_hap2.t2t_h9_v01_hap1.syn.link.bb visibility hide html ../html/empty.html group hsCompGeno priority 11 # intentionally left blank (common_mm2_genomic_aln.trackDb.txt) # minimap2 genomic alignments (common_cactus_genomic_aln.trackDb.txt) # needs common_genomic_aln_super.trackDb.txt included once track hs1_cactus_chain parent hs1_genomic_aln_super type bigChain hs1 shortLabel hs1 cactus chain longLabel hs1 cactus chain bigDataUrl cactus-genomic-aln/hs1/t2t_h9_v01_hap2.hs1.chain.bb linkDataUrl cactus-genomic-aln/hs1/t2t_h9_v01_hap2.hs1.link.bb visibility hide html ../html/empty.html group hsCompGeno priority 10 # intentionally left blank (common_cactus_genomic_aln.trackDb.txt) # minimap2 genomic alignments (common_cactus_genomic_aln.trackDb.txt) # needs common_genomic_aln_super.trackDb.txt included once track hg38_cactus_chain parent hg38_genomic_aln_super type bigChain hg38 shortLabel hg38 cactus chain longLabel hg38 cactus chain bigDataUrl cactus-genomic-aln/hg38/t2t_h9_v01_hap2.hg38.chain.bb linkDataUrl cactus-genomic-aln/hg38/t2t_h9_v01_hap2.hg38.link.bb visibility hide html ../html/empty.html group hsCompGeno priority 10 # intentionally left blank (common_cactus_genomic_aln.trackDb.txt) # minimap2 genomic alignments (common_cactus_genomic_aln.trackDb.txt) # needs common_genomic_aln_super.trackDb.txt included once track t2t_h9_v01_hap1_cactus_chain parent t2t_h9_v01_hap1_genomic_aln_super type bigChain t2t_h9_v01_hap1 shortLabel t2t_h9_v01_hap1 cactus chain longLabel t2t_h9_v01_hap1 cactus chain bigDataUrl cactus-genomic-aln/t2t_h9_v01_hap1/t2t_h9_v01_hap2.t2t_h9_v01_hap1.chain.bb linkDataUrl cactus-genomic-aln/t2t_h9_v01_hap1/t2t_h9_v01_hap2.t2t_h9_v01_hap1.link.bb visibility hide html ../html/empty.html group hsCompGeno priority 10 # intentionally left blank (common_cactus_genomic_aln.trackDb.txt) track sedefMappedSegDupsSuper superTrack on hide shortLabel Mapped SegDups longLabel Mapped Segmental Duplications group rep priority 100 track sedefSegDupsFiltSuper superTrack on hide shortLabel SegDups 90% & 98% longLabel Segmental Duplications filtered 90% & 98% group rep priority 110 track segdupVennSuper superTrack on hide shortLabel Segdup Venn longLabel Segdup Venn Analysis group rep priority 120 track sedef_map_hs1_dup_mm2 parent sedefMappedSegDupsSuper shortLabel Sedef hs1 map longLabel Sedef hs1 mapped bigDataUrl sedef-asm-map/hs1/t2t_h9_v01_hap2.hs1.mm2.bb group rep html ../html/empty.html type bigPsl color 128,10,92 canPack on searchIndex name visibility hide labelFields name defaultLabelFields name baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 priority 1010 track sedef_map_hs1_98 parent sedefSegDupsFiltSuper shortLabel Sedef hs1 map 98% longLabel Sedef hs1 mapped 98% bigDataUrl sedef-venn/asm/t2t_h9_v01_hap2.hs1.sedef-map.0.98.bb group rep html ../html/empty.html type bigBed 12 color 128,10,92 canPack on visibility hide priority 1020 track sedef_map_hs1_90 parent sedefSegDupsFiltSuper shortLabel Sedef hs1 map 90% longLabel Sedef hs1 mapped 90% bigDataUrl sedef-venn/asm/t2t_h9_v01_hap2.hs1.sedef-map.0.90.bb group rep html ../html/empty.html type bigBed 12 color 128,10,92 canPack on visibility hide priority 1021 track sedef_map_t2t_h9_v01_hap1_dup_mm2 parent sedefMappedSegDupsSuper shortLabel Sedef t2t_h9_v01_hap1 map longLabel Sedef t2t_h9_v01_hap1 mapped bigDataUrl sedef-asm-map/t2t_h9_v01_hap1/t2t_h9_v01_hap2.t2t_h9_v01_hap1.mm2.bb group rep html ../html/empty.html type bigPsl color 128,10,92 canPack on searchIndex name visibility hide labelFields name defaultLabelFields name baseColorUseSequence lfExtra indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 priority 1110 track sedef_map_t2t_h9_v01_hap1_98 parent sedefSegDupsFiltSuper shortLabel Sedef t2t_h9_v01_hap1 map 98% longLabel Sedef t2t_h9_v01_hap1 mapped 98% bigDataUrl sedef-venn/asm/t2t_h9_v01_hap2.t2t_h9_v01_hap1.sedef-map.0.98.bb group rep html ../html/empty.html type bigBed 12 color 128,10,92 canPack on visibility hide priority 1120 track sedef_map_t2t_h9_v01_hap1_90 parent sedefSegDupsFiltSuper shortLabel Sedef t2t_h9_v01_hap1 map 90% longLabel Sedef t2t_h9_v01_hap1 mapped 90% bigDataUrl sedef-venn/asm/t2t_h9_v01_hap2.t2t_h9_v01_hap1.sedef-map.0.90.bb group rep html ../html/empty.html type bigBed 12 color 128,10,92 canPack on visibility hide priority 1121 # segdupVennSuper track segdupVenn90_3-way_full_sets shortLabel Venn 90 3-way full sets longLabel Segdup Venn 90% 3-way full sets parent segdupVennSuper group rep visibility hide itemRgb on type bigBed 9 bigDataUrl sedef-venn/sets/hs1+t2t_h9_v01_hap1+t2t_h9_v01_hap2/t2t_h9_v01_hap2.0.90.full-sets.bb html ../html/empty.html priority 12100 filterLabel.name Subset filterValues.name annot,hs1,hap1,hap2,hap1,,hs1,hap2,,hs1,hap1,,hap2,hap1,,hap2,,hs1,union filterType.name multipleListOr # segdupVennSuper track segdupVenn90_3-way_full_regions shortLabel Venn 90 3-way full regions longLabel Segdup Venn 90% 3-way full regions parent segdupVennSuper group rep visibility hide itemRgb on type bigBed 9 bigDataUrl sedef-venn/sets/hs1+t2t_h9_v01_hap1+t2t_h9_v01_hap2/t2t_h9_v01_hap2.0.90.full-regions.bb html ../html/empty.html priority 13100 filterLabel.name Subset filterValues.name annot,hs1,hap1,hap2,hap1,,hs1,hap2,,hs1,hap1,,hap2,hap1,,hap2,,hs1,union filterType.name multipleListOr # segdupVennSuper track segdupVenn90_3-way_mzchain_sets shortLabel Venn 90 3-way mzchain sets longLabel Segdup Venn 90% 3-way mzchain sets parent segdupVennSuper group rep visibility hide itemRgb on type bigBed 9 bigDataUrl sedef-venn/sets/hs1+t2t_h9_v01_hap1+t2t_h9_v01_hap2/t2t_h9_v01_hap2.0.90.mzchain-sets.bb html ../html/empty.html priority 14100 filterLabel.name Subset filterValues.name annot,hs1,hap1,hap2,hap1,,hs1,hap2,,hs1,hap1,,hap2,hap1,,hap2,,hs1,union filterType.name multipleListOr # 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