hub GCA_900108605.1 genome assembly
shortLabel American mink (2018)
longLabel American mink (2018)/Neogale vison/GCA_900108605.1_NNQGG.v01 genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCA_900108605.1_NNQGG.v01.description.html
genome GCA_900108605.1
taxId 452646
groups groups.txt
description American mink (2018)
twoBitPath GCA_900108605.1.2bit
twoBitBptUrl GCA_900108605.1.2bit.bpt
chromSizes GCA_900108605.1.chrom.sizes.txt
chromAliasBb GCA_900108605.1.chromAlias.bb
organism NNQGG.v01 Jan. 2018
defaultPos FNWR01000001.1:13436921-13446921
scientificName Neogale vison
htmlPath html/GCA_900108605.1_NNQGG.v01.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/900/108/605/GCA_900108605.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/900/108/605/GCA_900108605.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/900/108/605/GCA_900108605.1
track assembly
longLabel Assembly
shortLabel Assembly
visibility hide
colorByStrand 150,100,30 230,170,40
color 150,100,30
altColor 230,170,40
bigDataUrl bbi/GCA_900108605.1_NNQGG.v01.assembly.bb
type bigBed 6
html html/GCA_900108605.1_NNQGG.v01.assembly
searchIndex name
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
group map
track gap
longLabel AGP gap
shortLabel Gap (AGP defined)
visibility hide
color 0,0,0
bigDataUrl bbi/GCA_900108605.1_NNQGG.v01.gap.bb
type bigBed 4
group map
html html/GCA_900108605.1_NNQGG.v01.gap
track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_900108605.1_NNQGG.v01.cytoBand.bb
track gc5Base
shortLabel GC Percent
longLabel GC Percent in 5-Base Windows
group map
visibility dense
autoScale Off
maxHeightPixels 128:36:16
graphTypeDefault Bar
gridDefault OFF
windowingFunction Mean
color 0,0,0
altColor 128,128,128
viewLimits 30:70
type bigWig 0 100
bigDataUrl bbi/GCA_900108605.1_NNQGG.v01.gc5Base.bw
html html/GCA_900108605.1_NNQGG.v01.gc5Base
track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_900108605.1_NNQGG.v01.tanDups
track gapOverlap
parent tanDups on
shortLabel Gap Overlaps
longLabel Paired exactly identical sequence on each side of a gap
bigDataUrl bbi/GCA_900108605.1_NNQGG.v01.gapOverlap.bb
type bigBed 12
track tandemDups
parent tanDups on
shortLabel Tandem Dups
longLabel Paired exactly identical sequence survey over entire genome assembly
bigDataUrl bbi/GCA_900108605.1_NNQGG.v01.tandemDups.bb
type bigBed 12
track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_900108605.1_NNQGG.v01.rmsk.bb
maxWindowToDraw 5000000
html html/GCA_900108605.1_NNQGG.v01.repeatMasker
track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_900108605.1_NNQGG.v01.simpleRepeat.bb
html html/GCA_900108605.1_NNQGG.v01.simpleRepeat
track cpgIslands
compositeTrack on
shortLabel CpG Islands
longLabel CpG Islands (Islands < 300 Bases are Light Green)
group regulation
visibility dense
type bigBed 4 +
html html/GCA_900108605.1_NNQGG.v01.cpgIslands
track cpgIslandExt
parent cpgIslands off
shortLabel CpG Islands
longLabel CpG Islands (Islands < 300 Bases are Light Green)
type bigBed 4 +
priority 1
bigDataUrl bbi/GCA_900108605.1_NNQGG.v01.cpgIslandExt.bb
track cpgIslandExtUnmasked
parent cpgIslands on
shortLabel Unmasked CpG
longLabel CpG Islands on All Sequence (Islands < 300 Bases are Light Green)
type bigBed 4 +
priority 2
bigDataUrl bbi/GCA_900108605.1_NNQGG.v01.cpgIslandExtUnmasked.bb
track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_900108605.1_NNQGG.v01.windowMasker.bb
html html/GCA_900108605.1_NNQGG.v01.windowMasker
track allGaps
shortLabel All Gaps
longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps
group map
visibility hide
type bigBed 3
bigDataUrl bbi/GCA_900108605.1_NNQGG.v01.allGaps.bb
html html/GCA_900108605.1_NNQGG.v01.allGaps
track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_900108605.1_NNQGG.v01.augustus.bb
html html/GCA_900108605.1_NNQGG.v01.augustus
track xenoRefGene
shortLabel RefSeq mRNAs
longLabel RefSeq mRNAs mapped to this assembly
group rna
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_900108605.1_NNQGG.v01.xenoRefGene.bb
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
labelFields name,geneName,geneName2
defaultLabelFields geneName
searchIndex name
searchTrix ixIxx/GCA_900108605.1_NNQGG.v01.xenoRefGene.ix
html html/GCA_900108605.1_NNQGG.v01.xenoRefGene
track ensGene
shortLabel Ensembl genes
longLabel Ensembl genes version 103/Feb. 2021
group genes
priority 40
visibility pack
color 150,0,0
itemRgb on
type bigBed 12 .
bigDataUrl bbi/GCA_900108605.1_NNQGG.v01.ensGene.bb
searchIndex name
baseColorUseCds given
baseColorDefault genomicCodons
html html/GCA_900108605.1_NNQGG.v01.ensGene
track HLTOGAannotvHg38v1
bigDataUrl bbi/HLTOGAannotVsHg38v1.bb
shortLabel TOGA vs. hg38
longLabel TOGA annotations using human/hg38 as reference
group genes
visibility pack
itemRgb on
type bigBed 12
searchIndex name
searchTrix ixIxx/HLTOGAannotVsHg38v1.ix
html html/TOGAannotation
track evaSnp8
shortLabel EVA SNP Release 8
longLabel Short Genetic Variants from European Variant Archive Release 8
type bigBed 9 +
visibility dense
group varRep
itemRgb on
bigDataUrl contrib/evaSnp8/evaSnp8.bb
url https://www.ebi.ac.uk/eva/?variant&accessionID=$$
searchIndex name
mouseOver Ref/Alt allele(s): $ref>$alt
Var type: $ucscClass
AA change: $aaChange
filterValues.varClass SNV|SNV,deletion|Deletion,indel|Indel,insertion|Insertion,MNV|MNV,sequence_alteration|Sequence alteration
filterLabel.varClass Variant class from EVA SO term
filterLabel.ucscClass Functional effect per UCSC Variant Annotation
filterValues.ucscClass downstream_gene_variant|Downstream gene variant,upstream_gene_variant|Upstream gene variant,intron_variant|Intron variant,NMD_transcript_variant|Nonsense-mediated mRNA decay (NMD) variant,5_prime_UTR_variant|5 prime UTR variant,3_prime_UTR_variant|3 prime UTR variant,missense_variant|Missense variant,synonymous_variant|Synonymous variant,non_coding_transcript_exon_variant|Non-coding transcript exon variant,no_sequence_alteration|No sequence alteration,splice_region_variant|Splice region variant,frameshift_variant|Frameshift variant,stop_gained|Stop gained,splice_acceptor_variant|Splice acceptor variant,inframe_deletion|Inframe deletion,inframe_insertion|Inframe insertion,splice_donor_variant|Splice donor variant,coding_sequence_variant|Coding sequence variant,initiator_codon_variant|Initiator codon variant,stop_lost|Stop lost,stop_retained_variant|Stop retained variant,intergenic_variant|Intergenic variant
filterType.ucscClass multipleListOnlyOr
filterValues.itemRgb 255,,0,,0|Protein-altering and splice variants,0,,128,,0|Synonymous variants,0,,0,,255|Non-coding transcripts or UTR variants,0,,0,,0|Intergenic and intronic variants
filterLabel.itemRgb General variant types by color grouping
maxWindowCoverage 250000
maxItems 1000000
html contrib/evaSnp8/description
track Tiberius
bigDataUrl contrib/tiberius/tiberius.bigGenePred.bb
shortLabel Tiberius genes
longLabel Tiberius ab initio gene prediction
type bigGenePred
visibility pack
color 0,102,204
noScoreFilter on
html contrib/tiberius/Tiberius.html
group genes
dataVersion Tiberius version 2025-01-07
baseColorDefault genomicCodons