[ { "id": "hs1", "blatDB": "hub_3671779_hs1", "name": "Human (T2T CHM13-v2.0/hs1)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/chm13v2.0/chm13v2.0.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/chm13v2.0/chm13v2.0.fa.fai", "cytobandBbURL": "https://hgdownload.soe.ucsc.edu/gbdb/hs1/cytoBandMapped/cytoBandMapped.bb", "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.chromAlias.txt", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.2bit", "twoBitBptURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.2bit.bpt", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.chrom.sizes.txt", "tracks": [ { "name": "RefSeq Curated", "type": "annotation", "format": "biggenepred", "url": "https://hgdownload.soe.ucsc.edu/gbdb/hs1/ncbiRefSeq/ncbiRefSeqCurated.bb", "trixURL": "https://hgdownload.soe.ucsc.edu/gbdb/hs1/ncbiRefSeq/ncbiRefSeqCurated.ix", "visibilityWindow": -1, "order": 1000000 }, { "id": "catLiftOffGenesV1", "name": "CAT/Liftoff Genes", "format": "bigbed", "description": " CAT + Liftoff Gene Annotations", "url": "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/bbi/GCA_009914755.4_T2T-CHM13v2.0.catLiftOffGenesV1/catLiftOffGenesV1.bb", "displayMode": "EXPANDED", "height": 200, "visibilityWindow": -1, "supportsWholeGenome": false, "order": 1000000 }, { "id": "augustus", "name": "Augustus", "format": "bigbed", "description": " Augustus Gene Predictions", "url": "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/bbi/GCA_009914755.4_T2T-CHM13v2.0.augustus.bb", "displayMode": "EXPANDED", "color": "rgb(180,0,0)", "height": 200, "visibilityWindow": -1, "supportsWholeGenome": false, "order": 1000001 }, { "name": "Genes", "format": "bed", "url": "https://igv.org/genomes/data/hs1/chm13v2.0_geneLocations.short.bed.gz", "hidden": true, "searchable": true } ] }, { "id": "chm13v1.1", "name": "Human (T2T CHM13-v1.1)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/t2t-chm13-v1.1/GCA_009914755.3_CHM13_T2T_v1.1_genomic.fna", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/t2t-chm13-v1.1/GCA_009914755.3_CHM13_T2T_v1.1_genomic.fna.fai", "cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/t2t-chm13-v1.1/cytoBandIdeo.bed", "tracks": [ { "name": "Annotations", "type": "annotation", "format": "bigbed", "url": "https://s3.amazonaws.com/igv.org.genomes/t2t-chm13-v1.1/CHM13.combined.v4.bb", "supportsWholeGenome": false, "height": 200, "displayMode": "EXPANDED", "order": 1000000, "description": "Annotations from UCSC.
blue - protein coding
green - non coding
pink - psuedo gene", "visibilityWindow": -1 }, { "name": "Genes", "format": "bed", "url": "https://s3.amazonaws.com/igv.org.genomes/t2t-chm13-v1.1/CHM13.names.bed.gz", "hidden": true, "searchable": true } ] }, { "id": "hg38", "name": "Human (GRCh38/hg38)", "fastaURL": "https://igv.org/genomes/data/hg38/hg38.fa", "indexURL": "https://igv.org/genomes/data/hg38/hg38.fa.fai", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBandIdeo.txt.gz", "aliasURL": "https://igv.org/genomes/data/hg38/hg38_alias.tab", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes", "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY", "tracks": [ { "name": "Refseq Curated", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeqCurated.txt.gz", "indexed": false, "order": 1000001, "infoURL": "https://www.ncbi.nlm.nih.gov/gene/?term=$$" } ] }, { "id": "hg38_1kg", "ucscID": "hg38", "blatDB": "hg38", "name": "Human (hg38 1kg/GATK)", "fastaURL": "https://1000genomes.s3.amazonaws.com/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa", "indexURL": "https://1000genomes.s3.amazonaws.com/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBandIdeo.txt.gz", "aliasURL": "https://igv.org/genomes/data/hg38/hg38_alias.tab", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes", "tracks": [ { "name": "Refseq Curated", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeqCurated.txt.gz", "indexed": false, "order": 1000000, "infoURL": "https://www.ncbi.nlm.nih.gov/gene/?term=$$" } ], "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY" }, { "id": "hg19", "name": "Human (GRCh37/hg19)", "fastaURL": "https://igv.org/genomes/data/hg19/hg19.fasta", "indexURL": "https://igv.org/genomes/data/hg19/hg19.fasta.fai", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz", "aliasURL": "https://igv.org/genomes/data/hg19/hg19_alias.tab", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes", "tracks": [ { "name": "Refseq Curated", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ncbiRefSeqCurated.txt.gz", "indexed": false, "order": 1000000, "infoURL": "https://www.ncbi.nlm.nih.gov/gene/?term=$$" } ], "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY" }, { "id": "hg18", "name": "Human (hg18)", "fastaURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg18/hg18.fasta", "indexURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg18/hg18.fasta.fai", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/cytoBandIdeo.txt.gz", "tracks": [ { "name": "Refseq Genes", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/refGene.txt.gz", "indexed": false, "visibilityWindow": -1, "order": 1000000, "searchable": true } ], "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY" }, { "id": "mm39", "name": "Mouse (GRCm39/mm39)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/mm39/mm39.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/mm39/mm39.fa.fai", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/cytoBandIdeo.txt.gz", "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.chromAlias.txt", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.chrom.sizes", "tracks": [ { "name": "Refseq Curated", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/ncbiRefSeqCurated.txt.gz", "indexed": false, "order": 1000000 } ], "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chrX,chrY" }, { "id": "mm10", "name": "Mouse (GRCm38/mm10)", "fastaURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/mm10/mm10.fa", "indexURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/mm10/mm10.fa.fai", "cytobandURL": "https://s3.amazonaws.com/igv.broadinstitute.org/annotations/mm10/cytoBandIdeo.txt.gz", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.chrom.sizes", "order": 1000000, "tracks": [ { "name": "Refseq Curated", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/ncbiRefSeqCurated.txt.gz", "indexed": false, "order": 1000000 } ], "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chrX,chrY" }, { "id": "mm9", "name": "Mouse (NCBI37/mm9)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/mm9/mm9.fasta", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/mm9/mm9.fasta.fai", "cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/mm9/cytoBandIdeo.txt.gz", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/mm9.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/mm9.chrom.sizes", "tracks": [ { "name": "Refseq Curated", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/refGene.txt.gz", "indexed": false, "order": 1000000 } ], "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chrX,chrY" }, { "id": "rn7", "name": "Rat (rn7) ", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/rn7/rn7.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/rn7/rn7.fa.fai", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/rn7/database/cytoBandIdeo.txt.gz", "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/rn7/bigZips/rn7.chromAlias.txt", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/rn7/bigZips/rn7.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/rn7/bigZips/rn7.chrom.sizes", "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chrX,chrY", "tracks": [ { "name": "Refseq Curated", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/rn7/database/ncbiRefSeqCurated.txt.gz", "order": 1000000 } ] }, { "id": "rn6", "name": "Rat (RGCS 6.0/rn6)", "fastaURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/rn6/rn6.fa", "indexURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/rn6/rn6.fa.fai", "cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/rn6/cytoBand.txt.gz", "order": 1000000, "tracks": [ { "name": "Refseq Genes", "format": "refgene", "url": "https://s3.amazonaws.com/igv.org.genomes/rn6/ncbiRefSeq.sorted.txt.gz", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/rn6/ncbiRefSeq.sorted.txt.gz.tbi", "order": 1000000, "supportsWholeGenome": false, "visibilityWindow": -1 }, { "name": "Genes", "format": "bed", "url": "https://s3.amazonaws.com/igv.org.genomes/locations/geneLocations_rn6.bed.gz", "hidden": true, "searchable": true } ] }, { "id": "gorGor6", "name": "Gorilla (Kamilah_GGO_v0/gorGor6) ", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/gorGor6/gorGor6.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/gorGor6/gorGor6.fa.fai", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/database/cytoBandIdeo.txt.gz", "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/bigZips/gorGor6.chromAlias.txt", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/bigZips/gorGor6.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/bigZips/gorGor6.chrom.sizes", "tracks": [ { "name": "Refseq Curated", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/database/ncbiRefSeqCurated.txt.gz", "order": 1000000 } ], "chromosomeOrder": "chr1,chr2A,chr2B,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX" }, { "id": "gorGor4", "name": "Gorilla (gorGor4.1/gorGor4)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/gorGor4/gorGor4.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/gorGor4/gorGor4.fa.fai", "cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/gorGor4/cytoBandIdeo.txt.gz", "tracks": [ { "name": "Refseq Curated", "format": "refgene", "url": "https://s3.amazonaws.com/igv.org.genomes/gorGor4/refGene.txt.gz", "indexed": false, "order": 1000000, "visibilityWindow": -1, "supportsWholeGenome": false } ], "chromosomeOrder": "chr1,chr2A,chr2B,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX" }, { "id": "panTro6", "name": "Chimp (panTro6) (panTro6)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/panTro6/panTro6.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/panTro6/panTro6.fa.fai", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/database/cytoBandIdeo.txt.gz", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/bigZips/panTro6.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/bigZips/panTro6.chrom.sizes", "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/bigZips/panTro6.chromAlias.txt", "nameSet": "ucsc", "chromosomeOrder": "chr1,chr2A,chr2B,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY", "tracks": [ { "name": "Refseq Curated", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/database/ncbiRefSeqCurated.txt.gz", "order": 1000000 } ] }, { "id": "panTro5", "name": "Chimp (panTro5) (panTro5)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/panTro5/panTro5.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/panTro5/panTro5.fa.fai", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro5/database/cytoBandIdeo.txt.gz", "chromosomeOrder": "chr1,chr2A,chr2B,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY", "tracks": [ { "name": "Refseq Genes", "format": "refgene", "url": "https://s3.amazonaws.com/igv.org.genomes/panTro5/ncbiRefSeq.txt.gz", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/panTro5/ncbiRefSeq.txt.gz.tbi", "order": 1000000, "visibilityWindow": -1, "supportsWholeGenome": false }, { "name": "Genes", "format": "bed", "url": "https://s3.amazonaws.com/igv.org.genomes/locations/geneLocations_panTro5.bed.gz", "hidden": true, "searchable": true } ] }, { "id": "panTro4", "name": " Chimp (SAC 2.1.4/panTro4)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/panTro4/panTro4.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/panTro4/panTro4.fa.fai", "cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/panTro4/cytoBandIdeo.txt.gz", "chromosomeOrder": "chr1,chr2A,chr2B,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY", "tracks": [ { "name": "Refseq Genes", "format": "refgene", "url": "https://s3.amazonaws.com/igv.org.genomes/panTro4/refGene.sorted.txt.gz", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/panTro4/refGene.sorted.txt.gz.tbi", "order": 1000000, "visibilityWindow": -1, "supportsWholeGenome": false }, { "name": "Genes", "format": "bed", "url": "https://s3.amazonaws.com/igv.org.genomes/locations/geneLocations_panTro4.bed.gz", "hidden": true, "searchable": true } ] }, { "id": "macFas5", "name": "Macaca fascicularis (macFas5)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/macFas5/macFas5.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/macFas5/macFas5.fa.fai", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/macFas5/database/cytoBandIdeo.txt.gz", "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/macFas5/bigZips/macFas5.chromAlias.txt", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/macFas5/bigZips/macFas5.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/macFas5/bigZips/macFas5.chrom.sizes", "tracks": [ { "name": "Genes", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/macFas5/database/ncbiRefSeqCurated.txt.gz", "order": 1000000 } ] }, { "id": "GCA_011100615.1", "blatDB": "GCA_011100615.1", "name": "Macaca fascicularis 6.0 (GCA_011100615.1)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/GCA_011100615.1/Macaca_fascicularis.Macaca_fascicularis_6.0.dna.toplevel.fa.gz", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/GCA_011100615.1/Macaca_fascicularis.Macaca_fascicularis_6.0.dna.toplevel.fa.gz.fai", "compressedIndexURL": "https://s3.amazonaws.com/igv.org.genomes/GCA_011100615.1/Macaca_fascicularis.Macaca_fascicularis_6.0.dna.toplevel.fa.gz.gzi", "aliasURL": "https://s3.amazonaws.com/igv.org.genomes/GCA_011100615.1/GCA_011100615.1_chromAlias.tab", "tracks": [ { "name": "Annotations", "format": "gff3", "description": " Ensembl gene annotation 8-11-2022", "url": "https://s3.amazonaws.com/igv.org.genomes/GCA_011100615.1/Macaca_fascicularis.Macaca_fascicularis_6.0.108.sorted.gff3.gz", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/GCA_011100615.1/Macaca_fascicularis.Macaca_fascicularis_6.0.108.sorted.gff3.gz.tbi", "visibilityWindow": -1, "displayMode": "EXPANDED", "height": 200 }, { "name": "Genes", "format": "bed", "url": "https://s3.amazonaws.com/igv.org.genomes/GCA_011100615.1/GCA_011100615.1_ucsc_ensGene.bed", "hidden": true, "searchable": true } ] }, { "id": "panPan2", "name": "Bonobo (MPI-EVA panpan1.1/panPan2)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/panPan2/panPan2.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/panPan2/panPan2.fa.fai", "cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/panPan2/cytoBandIdeo.txt.gz", "chromosomeOrder": "chr1,chr2A,chr2B,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX", "tracks": [ { "name": "Refseq Genes", "format": "refgene", "url": "https://s3.amazonaws.com/igv.org.genomes/panPan2/ncbiRefSeq.txt.gz", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/panPan2/ncbiRefSeq.txt.gz.tbi", "order": 1000000, "visibilityWindow": -1, "supportsWholeGenome": false }, { "name": "Genes", "format": "bed", "url": "https://s3.amazonaws.com/igv.org.genomes/locations/geneLocations_panPan2.bed.gz", "hidden": true, "searchable": true } ] }, { "id": "canFam6", "name": "Dog (canFam6) ", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam6/database/cytoBandIdeo.txt.gz", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam6/bigZips/canFam6.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam6/bigZips/canFam6.chrom.sizes", "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam6/bigZips/canFam6.chromAlias.txt", "nameSet": "ucsc", "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chr23,chr24,chr25,chr26,chr27,chr28,chr29,chr30,chr31,chr32,chr33,chr34,chr35,chr36,chr37,chr38,chrX", "tracks": [ { "name": "Refseq Curated", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam6/database/ncbiRefSeqCurated.txt.gz", "order": 1000000 } ] }, { "id": "canFam5", "name": "Dog (canFam5) ", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/canFam5/canFam5.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/canFam5/canFam5.fa.fai", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam5/database/cytoBandIdeo.txt.gz", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam5/bigZips/canFam5.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam5/bigZips/canFam5.chrom.sizes", "chromAliasBbURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam5/bigZips/canFam5.chromAlias.bb", "nameSet": "ucsc", "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chr23,chr24,chr25,chr26,chr27,chr28,chr29,chr30,chr31,chr32,chr33,chr34,chr35,chr36,chr37,chr38,chrX", "tracks": [ { "name": "Genes", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam5/database/refGene.txt.gz", "order": 1000000 } ] }, { "id": "canFam4", "name": "Dog (UU_Cfam_GSD_1.0/canFam4)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/canFam4/canFam4.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/canFam4/canFam4.fa.fai", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam4/database/cytoBandIdeo.txt.gz", "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam4/bigZips/canFam4.chromAlias.txt", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam4/bigZips/canFam4.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam4/bigZips/canFam4.chrom.sizes", "nameSet": "ucsc", "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chr23,chr24,chr25,chr26,chr27,chr28,chr29,chr30,chr31,chr32,chr33,chr34,chr35,chr36,chr37,chr38,chrX", "tracks": [ { "name": "RefSeq Curated", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam4/database/ncbiRefSeqCurated.txt.gz", "indexed": false, "order": 1000000 } ] }, { "id": "canFam3", "name": "Dog (Broad CanFam3.1/canFam3)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/canFam3/canFam3.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/canFam3/canFam3.fa.fai", "cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/canFam3/cytoBandIdeo.txt.gz", "tracks": [ { "name": "Refseq Genes", "format": "refgene", "url": "https://s3.amazonaws.com/igv.org.genomes/canFam3/ncbiRefSeq.sorted.txt.gz", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/canFam3/ncbiRefSeq.sorted.txt.gz.tbi", "indexed": false, "order": 1000000, "visibilityWindow": -1, "supportsWholeGenome": false }, { "name": "Genes", "format": "bed", "url": "https://s3.amazonaws.com/igv.org.genomes/locations/geneLocations_canFam3.bed.gz", "hidden": true, "searchable": true } ] }, { "id": "bosTau9", "name": "Cow (ARS-UCD1.2/bosTau9)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/bosTau9/bosTau9.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/bosTau9/bosTau9.fa.fai", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/database/cytoBandIdeo.txt.gz", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips/bosTau9.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips/bosTau9.chrom.sizes", "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips/bosTau9.chromAlias.txt", "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chr23,chr24,chr25,chr26,chr27,chr28,chr29,chrX", "tracks": [ { "name": "Refseq Curated", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/database/ncbiRefSeqCurated.txt.gz", "order": 1000000 } ] }, { "id": "bosTau8", "name": "Cow (UMD_3.1.1/bosTau8)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/bosTau8/bosTau8.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/bosTau8/bosTau8.fa.fai", "cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/bosTau8/cytoBandIdeo.txt.gz", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau8/bigZips/bosTau8.2bit", "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau8/bigZips/bosTau8.chromAlias.txt", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau8/bigZips/bosTau8.chrom.sizes", "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chr23,chr24,chr25,chr26,chr27,chr28,chr29,chrX", "tracks": [ { "name": "Refseq Genes", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau8/database/refGene.txt.gz", "indexed": false, "order": 1000000 } ] }, { "id": "susScr11", "name": "Pig (SGSC Sscrofa11.1/susScr11)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/susScr11/susScr11.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/susScr11/susScr11.fa.fai", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/susScr11/bigZips/susScr11.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/susScr11/bigZips/susScr11.chrom.sizes", "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/susScr11/bigZips/susScr11.chromAlias.txt", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/susScr11/database/cytoBandIdeo.txt.gz", "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chrX,chrY", "tracks": [ { "name": "Refseq Genes", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/susScr11/database/refGene.txt.gz", "indexed": false, "order": 1000000 } ] }, { "id": "galGal6", "name": " Chicken (galGal6)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/galGal6/galGal6.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/galGal6/galGal6.fa.fai", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/galGal6/database/cytoBandIdeo.txt.gz", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/galGal6/bigZips/galGal6.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/galGal6/bigZips/galGal6.chrom.sizes", "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/galGal6/bigZips/galGal6.chromAlias.txt", "tracks": [ { "name": "Refseq Curated", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/galGal6/database/ncbiRefSeqCurated.txt.gz", "order": 1000000 } ] }, { "id": "GCF_016699485.2", "name": "Gallus gallus (GCF_016699485.2)", "fastaURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/GCF_016699485.2/GCF_016699485.2.fa", "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/GCF_016699485.2/GCF_016699485.2.fa.fai", "aliasURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/GCF_016699485.2/GCF_016699485.2_chromAlias.tab", "blatDB": "GCF_016699485.2", "tracks": [ { "name": "Genes", "format": "bed", "url": "https://igv-genepattern-org.s3.amazonaws.com/genomes/GCF_016699485.2/GCF_016699485.2_gene_names.bed", "hidden": true, "displayMode": "COLLAPSED" }, { "id": "ncbiRefSeqCurated", "name": "RefSeq Transcripts", "description": " NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*)", "url": "https://hgdownload.gi.ucsc.edu/hubs/birds/../GCF/016/699/485/GCF_016699485.2/bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.ncbiRefSeqCurated.bb", "displayMode": "EXPANDED", "color": "rgb(12,12,120)", "parent": "refSeqComposite on", "height": 300 } ] }, { "id": "danRer11", "name": "Zebrafish (GRCZ11/danRer11)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/danRer11/danRer11.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/danRer11/danRer11.fa.fai", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/danRer11/database/cytoBandIdeo.txt.gz", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/danRer11/bigZips/danRer11.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/danRer11/bigZips/danRer11.chrom.sizes", "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/danRer11/bigZips/danRer11.chromAlias.txt", "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chr23,chr24,chr25", "tracks": [ { "name": "Refseq Curated", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/danRer11/database/ncbiRefSeqCurated.txt.gz", "order": 1000000 } ] }, { "id": "danRer10", "name": "Zebrafish (GRCZ10/danRer10)", "fastaURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/danRer10/danRer10.fa", "indexURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/danRer10/danRer10.fa.fai", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/danRer10/database/cytoBandIdeo.txt.gz", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/danRer10/bigZips/danRer10.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/danRer10/bigZips/danRer10.chrom.sizes", "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/danRer10/bigZips/danRer10.chromAlias.txt", "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chr23,chr24,chr25", "order": 1000000, "tracks": [ { "name": "Refseq Curated", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/danRer10/database/ncbiRefSeqCurated.txt.gz", "order": 1000000, "searchable": true } ] }, { "id": "ce11", "name": "C. elegans (ce11)", "fastaURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/ce11/ce11.fa", "indexURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/ce11/ce11.fa.fai", "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/ce11/database/cytoBandIdeo.txt.gz", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/ce11/bigZips/ce11.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/ce11/bigZips/ce11.chrom.sizes", "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/ce11/bigZips/ce11.chromAlias.txt", "chromosomeOrder": "chrI,chrII,chrIII,chrIV,chrV,chrX", "tracks": [ { "name": "Refseq Curated", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/ce11/database/ncbiRefSeqCurated.txt.gz", "indexed": false, "order": 1000000, "searchable": true } ] }, { "id": "dm6", "name": "D. melanogaster (dm6)", "fastaURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/dm6/dm6.fa", "indexURL": "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/dm6/dm6.fa.fai", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/dm6.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/dm6.chrom.sizes", "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/dm6.chromAlias.txt", "chromosomeOrder": "chr2L,chr2R,chr3L,chr3R,chr4,chrX,chrY", "tracks": [ { "name": "Refseq Curated", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/dm6/database/ncbiRefSeqCurated.txt.gz", "indexed": false, "order": 1000000, "searchable": true } ] }, { "id": "dm3", "name": "D. melanogaster (dm3)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/dm3/dm3.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/dm3/dm3.fa.fai", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/dm3.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/dm3.chrom.sizes", "chromosomeOrder": "chr2L,chr2R,chr3L,chr3R,chr4,chrX", "tracks": [ { "name": "Refseq Curated", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/dm3/database/refGene.txt.gz", "indexed": false, "order": 1000000, "searchable": true } ] }, { "id": "dmel_r5.9", "name": "D. melanogaster (dmel_r5.9)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/dmel_r5.9/dmel-all-chromosome-r5.9.fasta", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/dmel_r5.9/dmel-all-chromosome-r5.9.fasta.fai", "tracks": [ { "name": "Transcripts", "format": "gff3", "url": "https://s3.amazonaws.com/igv.org.genomes/dmel_r5.9/dmel-r5.9.transcripts.sorted.gff.gz", "indexed": false, "order": 1000000, "searchable": true } ] }, { "id": "sacCer3", "name": "S. cerevisiae (sacCer3)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/sacCer3/sacCer3.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/sacCer3/sacCer3.fa.fai", "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/bigZips/sacCer3.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/bigZips/sacCer3.chrom.sizes", "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/bigZips/sacCer3.chromAlias.txt", "chromosomeOrder": "chrI,chrII, chrIII,chrIV,chrV,chrVI,chrVII,chrVIII,chrIX,chrX,chrXI,chrXII,chrXIII,chrXIV,chrXV,chrXVI", "tracks": [ { "name": "Refseq Curated", "type": "annotation", "format": "refgene", "displayMode": "EXPANDED", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/database/ncbiRefSeqCurated.txt.gz", "indexed": false, "searchable": true } ] }, { "id": "ASM294v2", "name": "S. pombe (ASM294v2)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/ASM294v2/Schizosaccharomyces_pombe_all_chromosomes.fa", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/ASM294v2/Schizosaccharomyces_pombe_all_chromosomes.fa.fai", "twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/945/GCF_000002945.1/GCF_000002945.1.2bit", "nameSet": "ucsc", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/945/GCF_000002945.1/GCF_000002945.1.chrom.sizes.txt", "aliasURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/945/GCF_000002945.1/GCF_000002945.1.chromAlias.txt", "twoBitBptURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/945/GCF_000002945.1/GCF_000002945.1.2bit.bpt", "cytobandBbURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/945/GCF_000002945.1/bbi/GCF_000002945.1_ASM294v2.cytoBand.bb", "tracks": [ { "type": "annotation", "name": "RefSeq Curated", "format": "biggenepred", "url": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/945/GCF_000002945.1/bbi/GCF_000002945.1_ASM294v2.ncbiRefSeqCurated.bb", "displayMode": "EXPANDED", "description": "NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*)", "searchIndex": "name", "trixURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/945/GCF_000002945.1/ixIxx/GCF_000002945.1_ASM294v2.ncbiRefSeqCurated.ix", "visibilityWindow": -1 } ] }, { "id": "ASM985889v3", "name": "Sars-CoV-2 (ASM985889v3)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna.fai", "aliasURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/009/858/895/GCF_009858895.2/GCF_009858895.2.chromAlias.txt", "twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/009/858/895/GCF_009858895.2/GCF_009858895.2.2bit", "nameSet": "ucsc", "chromAliasBbURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/009/858/895/GCF_009858895.2/GCF_009858895.2.chromAlias.bb", "twoBitBptURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/009/858/895/GCF_009858895.2/GCF_009858895.2.2bit.bpt", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/009/858/895/GCF_009858895.2/GCF_009858895.2.chrom.sizes.txt", "description": "SARS-CoV-2 (Jan 2020 COVID-19)\nSevere acute respiratory syndrome coronavirus 2/GCF_009858895.2_ASM985889v3 genome assembly", "tracks": [ { "name": "NCBI Genes", "format": "biggenepred", "url": "https://hgdownload.soe.ucsc.edu/hubs/GCF/009/858/895/GCF_009858895.2/bbi/GCF_009858895.2_ASM985889v3.ncbiGene.bb", "displayMode": "EXPANDED", "description": "NCBI gene predictions", "color": "rgb(0,80,150)", "altColor": "rgb(150,80,0)", "infoURL": "https://www.ncbi.nlm.nih.gov/gene/?term=$$", "searchIndex": "name", "trixURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/009/858/895/GCF_009858895.2/ixIxx/GCF_009858895.2_ASM985889v3.ncbiGene.ix", "type": "annotation", "height": 70, "visibilityWindow": -1 } ] }, { "id": "tair10", "name": "A. thaliana (TAIR 10)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/tair10/TAIR10_chr_all.fas", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/tair10/TAIR10_chr_all.fas.fai", "twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/735/GCF_000001735.3/GCF_000001735.3.2bit", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/735/GCF_000001735.3/GCF_000001735.3.chrom.sizes.txt", "aliasURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/735/GCF_000001735.3/GCF_000001735.3.chromAlias.txt", "nameSet": "ucsc", "chromosomeOrder": "NC_003070.9,NC_003071.7,NC_003074.8,NC_003075.7,NC_003076.8", "tracks": [ { "name": "RefSeq Genes", "format": "gtf", "url": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/735/GCF_000001735.3/genes/GCF_000001735.3_TAIR10.ncbiRefSeq.gtf.gz", "indexed": false, "order": 1000000, "searchable": true } ] }, { "id": "GCA_003086295.2", "name": "Peanut (GCA_003086295.2)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/GCA_003086295.2/GCF_003086295.2_arahy.Tifrunner.gnm1.KYV3_genomic.fna", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/GCA_003086295.2/GCF_003086295.2_arahy.Tifrunner.gnm1.KYV3_genomic.fna.fai", "tracks": [ { "name": "Annotations", "format": "gff3", "url": "https://s3.amazonaws.com/igv.org.genomes/GCA_003086295.2/GCF_003086295.2_arahy.Tifrunner.gnm1.KYV3_genomic.gff.gz", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/GCA_003086295.2/GCF_003086295.2_arahy.Tifrunner.gnm1.KYV3_genomic.gff.gz.tbi", "order": 1000000, "visibilityWindow": -1, "supportsWholeGenome": false, "displayMode": "EXPANDED", "height": 300 } ] }, { "id": "GCF_001433935.1", "name": "O. sativa IRGSP-1.0 (GCF_001433935.1)", "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/GCF_001433935.1/GCF_001433935.1_IRGSP-1.0_genomic.fna.gz", "indexURL": "https://s3.amazonaws.com/igv.org.genomes/GCF_001433935.1/GCF_001433935.1_IRGSP-1.0_genomic.fna.gz.fai", "compressedIndexURL": "https://s3.amazonaws.com/igv.org.genomes/GCF_001433935.1/GCF_001433935.1_IRGSP-1.0_genomic.fna.gz.gzi", "aliasURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/001/433/935/GCF_001433935.1/GCF_001433935.1.chromAlias.txt", "twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/001/433/935/GCF_001433935.1/GCF_001433935.1.2bit", "twoBitBptURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/001/433/935/GCF_001433935.1/GCF_001433935.1.2bit.bpt", "description": "Japanese rice (Nipponbare 2015)\nOryza sativa Japonica Group/GCF_001433935.1_IRGSP-1.0 genome assembly", "nameSet": "ucsc", "chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/001/433/935/GCF_001433935.1/GCF_001433935.1.chrom.sizes.txt", "chromosomeOrder": "NC_029256.1,NC_029257.1,NC_029258.1,NC_029259.1,NC_029260.1,NC_029261.1,NC_029262.1,NC_029263.1,NC_029264.1,NC_029265.1,NC_029266.1,NC_029267.1", "tracks": [ { "name": "MSU V7 genes", "format": "gff3", "description": " Rice Genome Annotation Project", "url": "https://s3.amazonaws.com/igv.org.genomes/GCF_001433935.1/MSU_V7.gff3.gz", "displayMode": "EXPANDED", "height": 200 } ] }, { "id": "NC_016856.1", "name": "Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S", "fastaURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/NC_016856.1/NC_016856.1.fna", "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/NC_016856.1/NC_016856.1.fna.fai", "aliasURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/NC_016856.1/NC_016856.1_alias.tab", "tracks": [ { "url": "https://igv-genepattern-org.s3.amazonaws.com/genomes/NC_016856.1/NC_016856.1.gff.gz", "name": "NC_016856.1.gff.gz", "format": "gff3", "type": "annotation", "searchable": true } ] }, { "id": "GCA_000182895.1", "name": "Coprinopsis cinerea okayama7#130 (GCA_000182895.1)", "fastaURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/GCA_000182895.1/GCA_000182895.1.fa", "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/GCA_000182895.1/GCA_000182895.1.fa.fai", "aliasURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/GCA_000182895.1/GCA_000182895.1_chromAlias.tab", "blatDB": "GCA_000182895.1", "tracks": [ { "id": "ncbiGene", "name": "Gene models", "format": "bigGenePred", "description": " Gene models submitted to NCBI", "url": "https://hgdownload.soe.ucsc.edu/hubs/GCA/000/182/895/GCA_000182895.1/bbi/GCA_000182895.1_CC3.ncbiGene.bb", "displayMode": "EXPANDED", "color": "rgb(0,80,150)", "altColor": "rgb(0,150,80)", "colorBy": "strand", "infoURL": "https://hgdownload.soe.ucsc.edu/hubs/GCA/000/182/895/GCA_000182895.1/https://www.ncbi.nlm.nih.gov/gene/?term=$$" } ] } ]