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config_minus_wormbase.json
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config_minus_wormbase.json
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{
"plugins" : [
{
"name" : "VariantColorPlugin",
"umdLoc" : {
"uri" : "variantColor_plugin.js"
}
},
{
"name" : "HTVariantColorPlugin",
"umdLoc" : {
"uri" : "htVariantColor_plugin.js"
}
},
{
"name" : "MultiVariantColorPlugin",
"umdLoc" : {
"uri" : "multiVariartColor_plugin.js"
}
},
{
"name" : "VariantLabelPlugin",
"umdLoc" : {
"uri" : "variantLabel_plugin.js"
}
},
{
"name" : "VariantDescriptionPlugin",
"umdLoc" : {
"uri" : "variantDescription_plugin.js"
}
}
],
"aggregateTextSearchAdapters" : [
{
"namesIndexLocation" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/docker/5.4.0/FlyBase/fruitfly/names/"
},
"assemblyNames" : [
"Drosophila_melanogaster"
],
"type" : "JBrowse1TextSearchAdapter",
"textSearchAdapterId" : "fruitfly_generate-names-index"
},
{
"namesIndexLocation" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/docker/5.4.0/RGD/rat/names/"
},
"assemblyNames" : [
"Rattus_norvegicus"
],
"type" : "JBrowse1TextSearchAdapter",
"textSearchAdapterId" : "rat_generate-names-index"
},
{
"namesIndexLocation" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/docker/5.4.0/MGI/mouse/names/"
},
"assemblyNames" : [
"Mus_musculus"
],
"type" : "JBrowse1TextSearchAdapter",
"textSearchAdapterId" : "mouse_generate-names-index"
},
{
"namesIndexLocation" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/docker/5.4.0/human/names/"
},
"assemblyNames" : [
"Homo_sapiens"
],
"type" : "JBrowse1TextSearchAdapter",
"textSearchAdapterId" : "human_generate-names-index"
},
{
"namesIndexLocation" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/docker/5.4.0/zfin/zebrafish-11/names/"
},
"assemblyNames" : [
"Danio_rerio"
],
"type" : "JBrowse1TextSearchAdapter",
"textSearchAdapterId" : "zebrafish_generate-names-index"
},
{
"namesIndexLocation" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/docker/5.4.0/WormBase/c_elegans_PRJNA13758/names/"
},
"assemblyNames" : [
"Caenorhabditis_elegans"
],
"type" : "JBrowse1TextSearchAdapter",
"textSearchAdapterId" : "worm_generate-names-index"
},
{
"namesIndexLocation" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/docker/5.4.0/XenBase/x_laevis/names/"
},
"assemblyNames" : [
"Xenopus_laevis"
],
"type" : "JBrowse1TextSearchAdapter",
"textSearchAdapterId" : "xlaevis_generate-names-index"
},
{
"namesIndexLocation" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/docker/5.4.0/XenBase/x_tropicalis/names/"
},
"assemblyNames" : [
"Xenopus_tropicalis"
],
"type" : "JBrowse1TextSearchAdapter",
"textSearchAdapterId" : "xtropicalis_generate-names-index"
},
{
"namesIndexLocation" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/docker/5.4.0/SGD/yeast/names/"
},
"assemblyNames" : [
"Saccharomyces_cerevisiae"
],
"type" : "JBrowse1TextSearchAdapter",
"textSearchAdapterId" : "yeast_generate-names-index"
}
],
"assemblies": [
{
"name": "Homo_sapiens",
"displayName": "Homo sapiens",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "Homo_sapiens_refseq",
"adapter": {
"type": "BgzipFastaAdapter",
"fastaLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001405.40_GRCh38.p14_genomic.fna.gz"
},
"faiLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001405.40_GRCh38.p14_genomic.fna.gz.fai"
},
"metadataLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001405.40_GRCh38.p14_genomic.yaml"
},
"gziLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001405.40_GRCh38.p14_genomic.fna.gz.gzi"
}
},
"displays": [
{
"type": "LinearReferenceSequenceDisplay",
"displayId": "Homo_sapiens_refseq-LinearReferenceSequenceDisplay"
},
{
"type": "LinearGCContentDisplay",
"displayId": "Homo_sapiens_refseq-LinearGCContentDisplay"
}
]
}
},
{
"name": "Danio_rerio",
"displayName": "Danio rerio",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "Danio_rerio_refseq",
"adapter": {
"type": "BgzipFastaAdapter",
"fastaLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002035.6_GRCz11_genomic.fna.gz"
},
"faiLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002035.6_GRCz11_genomic.fna.gz.fai"
},
"metadataLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002035.6_GRCz11_genomic.yaml"
},
"gziLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002035.6_GRCz11_genomic.fna.gz.gzi"
}
},
"displays": [
{
"type": "LinearReferenceSequenceDisplay",
"displayId": "Danio_rerio_refseq-LinearReferenceSequenceDisplay"
},
{
"type": "LinearGCContentDisplay",
"displayId": "Danio_rerio_refseq-LinearGCContentDisplay"
}
]
}
},
{
"name": "Rattus_norvegicus",
"displayName": "Rattus norvegicus",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "Rattus_norvegicus_refseq",
"adapter": {
"type": "BgzipFastaAdapter",
"fastaLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_015227675.2_mRatBN7.2_genomic.fna.gz"
},
"faiLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_015227675.2_mRatBN7.2_genomic.fna.gz.fai"
},
"metadataLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_015227675.2_mRatBN7.2_genomic.yaml"
},
"gziLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_015227675.2_mRatBN7.2_genomic.fna.gz.gzi"
}
},
"displays": [
{
"type": "LinearReferenceSequenceDisplay",
"displayId": "Rattus_norvegicus_refseq-LinearReferenceSequenceDisplay"
},
{
"type": "LinearGCContentDisplay",
"displayId": "Rattus_norvegicus_refseq-LinearGCContentDisplay"
}
]
}
},
{
"name": "Mus_musculus",
"displayName": "Mus musculus",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "Mus_musculus_refseq",
"adapter": {
"type": "BgzipFastaAdapter",
"fastaLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001635.27_GRCm39_genomic.fna.gz"
},
"faiLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001635.27_GRCm39_genomic.fna.gz.fai"
},
"metadataLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001635.27_GRCm39_genomic.yaml"
},
"gziLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001635.27_GRCm39_genomic.fna.gz.gzi"
}
},
"displays": [
{
"type": "LinearReferenceSequenceDisplay",
"displayId": "Mus_musculus_refseq-LinearReferenceSequenceDisplay"
},
{
"type": "LinearGCContentDisplay",
"displayId": "Mus_musculus_refseq-LinearGCContentDisplay"
}
]
}
},
{
"name": "Xenopus_laevis",
"displayName": "Xenopus laevis",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "Xenopus_laevis_refseq",
"adapter": {
"type": "BgzipFastaAdapter",
"fastaLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/XENLA_9.2_genome.fa.gz"
},
"faiLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/XENLA_9.2_genome.fa.gz.fai"
},
"metadataLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/XENLA_9.2_genome.yaml"
},
"gziLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/XENLA_9.2_genome.fa.gz.gzi"
}
},
"displays": [
{
"type": "LinearReferenceSequenceDisplay",
"displayId": "Xenopus_laevis_refseq-LinearReferenceSequenceDisplay"
},
{
"type": "LinearGCContentDisplay",
"displayId": "Xenopus_laevis_refseq-LinearGCContentDisplay"
}
]
}
},
{
"name": "Xenopus_tropicalis",
"displayName": "Xenopus tropicalis",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "Xenopus_tropicalis_refseq",
"adapter": {
"type": "BgzipFastaAdapter",
"fastaLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/XENTR_9.1_genome.fa.gz"
},
"faiLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/XENTR_9.1_genome.fa.gz.fai"
},
"metadataLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/XENTR_9.1_genome.yaml"
},
"gziLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/XENTR_9.1_genome.fa.gz.gzi"
}
},
"displays": [
{
"type": "LinearReferenceSequenceDisplay",
"displayId": "Xenopus_tropicalis_refseq-LinearReferenceSequenceDisplay"
},
{
"type": "LinearGCContentDisplay",
"displayId": "Xenopus_tropicalis_refseq-LinearGCContentDisplay"
}
]
}
},
{
"name": "Caenorhabditis_elegans",
"displayName": "Caenorhabditis elegans",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "Caenorhabditis_elegans_refseq",
"adapter": {
"type": "BgzipFastaAdapter",
"fastaLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002985.6_WBcel235_genomic.fna.gz"
},
"faiLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002985.6_WBcel235_genomic.fna.gz.fai"
},
"metadataLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002985.6_WBcel235_genomic.yaml"
},
"gziLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002985.6_WBcel235_genomic.fna.gz.gzi"
}
},
"displays": [
{
"type": "LinearReferenceSequenceDisplay",
"displayId": "Caenorhabditis_elegans_refseq-LinearReferenceSequenceDisplay"
},
{
"type": "LinearGCContentDisplay",
"displayId": "Caenorhabditis_elegans_refseq-LinearGCContentDisplay"
}
]
}
},
{
"name": "Drosophila_melanogaster",
"displayName": "Drosophila melanogaster",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "Drosophila_melanogaster_refseq",
"adapter": {
"type": "BgzipFastaAdapter",
"fastaLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.gz"
},
"faiLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.gz.fai"
},
"metadataLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.yaml"
},
"gziLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.gz.gzi"
}
},
"displays": [
{
"type": "LinearReferenceSequenceDisplay",
"displayId": "Drosophila_melanogaster_refseq-LinearReferenceSequenceDisplay"
},
{
"type": "LinearGCContentDisplay",
"displayId": "Drosophila_melanogaster_refseq-LinearGCContentDisplay"
}
]
}
},
{
"name": "Saccharomyces_cerevisiae",
"displayName": "Saccharomyces cerevisiae",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "Saccharomyces_cerevisiae_refseq",
"adapter": {
"type": "BgzipFastaAdapter",
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