hub GCF_000146045.2 genome assembly
shortLabel baker's yeast S288C (2014)
longLabel baker's yeast S288C (2014)/Saccharomyces cerevisiae S288C/GCF_000146045.2_R64 genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCF_000146045.2_R64.description.html

genome GCF_000146045.2
taxId 559292
groups groups.txt
description baker's yeast S288C (2014)
twoBitPath GCF_000146045.2.2bit
twoBitBptUrl GCF_000146045.2.2bit.bpt
chromSizes GCF_000146045.2.chrom.sizes.txt
chromAliasBb GCF_000146045.2.chromAlias.bb
chromAuthority ucsc
organism R64 Dec. 2014
defaultPos NC_001136.10:510644-520644
scientificName Saccharomyces cerevisiae S288C
htmlPath html/GCF_000146045.2_R64.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/146/045/GCF_000146045.2
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/146/045/GCF_000146045.2
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/146/045/GCF_000146045.2
liftOver.GCF_000002945.1 liftOver/GCF_000146045.2ToGCF_000002945.1.over.chain.gz

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/GCF_000146045.2_R64.assembly.bb
type bigBed 6
html html/GCF_000146045.2_R64.assembly
searchIndex name
searchTrix ixIxx/GCF_000146045.2_R64.assembly.ix
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
group map

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_000146045.2_R64.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/GCF_000146045.2_R64.gc5Base.bw
html html/GCF_000146045.2_R64.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCF_000146045.2_R64.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCF_000146045.2_R64.tandemDups.bb
    type bigBed 12

track repeatMasker
compositeTrack on
shortLabel RepeatMasker
longLabel Repeating Elements by RepeatMasker
group varRep
visibility dense
type bigBed 6 +
colorByStrand 50,50,150 150,50,50
maxWindowToDraw 10000000
spectrum on
html html/GCF_000146045.2_R64.repeatMasker

    track repeatMaskerLTR
    parent repeatMasker
    shortLabel LTR
    longLabel LTR Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 3
    bigDataUrl bbi/GCF_000146045.2_R64.rmsk.LTR.bb

    track repeatMaskerSimple
    parent repeatMasker
    shortLabel Simple
    longLabel Simple Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 5
    bigDataUrl bbi/GCF_000146045.2_R64.rmsk.Simple.bb

    track repeatMaskerLowComplexity
    parent repeatMasker
    shortLabel Low Complexity
    longLabel Low Complexity Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 6
    bigDataUrl bbi/GCF_000146045.2_R64.rmsk.Low_complexity.bb

    track repeatMaskerRNA
    parent repeatMasker
    shortLabel RNA
    longLabel RNA Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 8
    bigDataUrl bbi/GCF_000146045.2_R64.rmsk.RNA.bb

    track repeatMaskerOther
    parent repeatMasker
    shortLabel Other
    longLabel Other Repeating Elements by RepeatMasker
    type bigBed 6 +
    priority 9
    bigDataUrl bbi/GCF_000146045.2_R64.rmsk.Other.bb

track repeatModeler
shortLabel RepeatModeler
longLabel RepeatModeler Repetitive Elements
type bigRmsk 9 +
visibility hide
group varRep
bigDataUrl bbi/GCF_000146045.2_R64.rModel.bb
xrefDataUrl bbi/GCF_000146045.2_R64.rModel.align.bb
maxWindowToDraw 5000000
html html/GCF_000146045.2_R64.repeatModeler

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCF_000146045.2_R64.simpleRepeat.bb
html html/GCF_000146045.2_R64.simpleRepeat

track refSeqComposite
compositeTrack on
shortLabel NCBI RefSeq
longLabel RefSeq gene predictions from NCBI
group genes
visibility pack
type bigBed
dragAndDrop subTracks
allButtonPair on
dataVersion SGD R64-5-1 (2025-03-09)
html html/GCF_000146045.2_R64.refSeqComposite
priority 2

        track ncbiRefSeq
        parent refSeqComposite on
        color 12,12,120
        shortLabel RefSeq All
        type bigGenePred
        urls name2="https://www.ncbi.nlm.nih.gov/gene/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$"
        labelFields name2,geneName,geneName2
        defaultLabelFields name2
        searchIndex name
        searchTrix ixIxx/GCF_000146045.2_R64.ncbiRefSeq.ix
        bigDataUrl bbi/GCF_000146045.2_R64.ncbiRefSeq.bb
        longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*)
        idXref ncbiRefSeqLink mrnaAcc name
        baseColorUseCds given
        baseColorDefault genomicCodons
        priority 1

        track ncbiRefSeqCurated
        color 12,12,120
        parent refSeqComposite on
        shortLabel RefSeq Curated
        longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*)
        type bigGenePred
        urls name2="https://www.ncbi.nlm.nih.gov/gene/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$"
        labelFields name2,geneName,geneName2
        defaultLabelFields name2
        searchIndex name
        searchTrix ixIxx/GCF_000146045.2_R64.ncbiRefSeqCurated.ix
        idXref ncbiRefSeqLink mrnaAcc name
        bigDataUrl bbi/GCF_000146045.2_R64.ncbiRefSeqCurated.bb
        baseColorUseCds given
        baseColorDefault genomicCodons
        priority 2

        track ncbiRefSeqOther
        color 32,32,32
        parent refSeqComposite on
        shortLabel RefSeq Other
        longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*)
        priority 4
        searchIndex name
        searchTrix ixIxx/GCF_000146045.2_R64.ncbiRefSeqOther.ix
        bigDataUrl bbi/GCF_000146045.2_R64.ncbiRefSeqOther.bb
        type bigBed 12 +
        labelFields name
        skipEmptyFields on
        urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/$$" HGNC="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" FlyBase="http://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="http://www.informatics.jax.org/marker/$$"

        track ncbiRefSeqPsl
        priority 5
        parent refSeqComposite off
        shortLabel RefSeq Alignments
        longLabel RefSeq Alignments of RNAs
        type bigPsl
        searchIndex name
        bigDataUrl bbi/GCF_000146045.2_R64.bigPsl.bb
        indelDoubleInsert on
        indelQueryInsert on
        showDiffBasesAllScales .
        showDiffBasesMaxZoom 10000.0
        showCdsMaxZoom 10000.0
        showCdsAllScales .
        baseColorDefault diffCodons
        pslSequence no
        baseColorUseSequence lfExtra
        baseColorUseCds table given
        color 0,0,0

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/GCF_000146045.2_R64.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/GCF_000146045.2_R64.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/GCF_000146045.2_R64.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCF_000146045.2_R64.windowMasker.bb
html html/GCF_000146045.2_R64.windowMasker

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCF_000146045.2_R64.augustus.bb
html html/GCF_000146045.2_R64.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/GCF_000146045.2_R64.xenoRefGene.bb
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
labelFields name,geneName,geneName2
defaultLabelFields geneName
searchIndex name
searchTrix ixIxx/GCF_000146045.2_R64.xenoRefGene.ix
html html/GCF_000146045.2_R64.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/GCF_000146045.2_R64.ensGene.bb
searchIndex name
baseColorUseCds given
baseColorDefault genomicCodons
html html/GCF_000146045.2_R64.ensGene

##############################################################################
# GCF_000002945.1 - brewer's yeast - Saccharomyces cerevisiae S288C - taxId: 559292
##############################################################################
track chainNetGCF_000002945.1
compositeTrack on
shortLabel brewer's yeast Chain/Net
longLabel brewer's yeast (2014-12-17), Chain and Net Alignments
subGroup1 view Views chain=Chain net=Net
dragAndDrop subTracks
visibility hide
group compGeno
priority 100.1
color 0,0,0
altColor 100,50,0
type bed 3
sortOrder view=+
otherDb GCF_000002945.1
html html/GCF_000146045.2_R64.chainNet

    track chainNetGCF_000002945.1Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetGCF_000002945.1
    spectrum on

        track chainGCF_000002945.1
        parent chainNetGCF_000002945.1Viewchain
        subGroups view=chain
        shortLabel brewer's yeast Chain
        longLabel brewer's yeast (2014-12-17) Chained Alignments
        type bigChain GCF_000002945.1
        bigDataUrl bbi/GCF_000146045.2_R64.chainGCF_000002945.1.bb
        linkDataUrl bbi/GCF_000146045.2_R64.chainGCF_000002945.1Link.bb
        priority 1

        track chainSynGCF_000002945.1
        parent chainNetGCF_000002945.1Viewchain
        subGroups view=chain
        shortLabel brewer's yeast synChain
        longLabel brewer's yeast (2014-12-17) Syntenic Chained Alignments
        type bigChain GCF_000002945.1
        bigDataUrl bbi/GCF_000146045.2_R64.chainSynGCF_000002945.1.bb
        linkDataUrl bbi/GCF_000146045.2_R64.chainSynGCF_000002945.1Link.bb
        priority 2

        track chainRBestGCF_000002945.1
        parent chainNetGCF_000002945.1Viewchain
        subGroups view=chain
        shortLabel brewer's yeast rbChain
        longLabel brewer's yeast (2014-12-17) Reciprocal Best Chained Alignments
        type bigChain GCF_000002945.1
        bigDataUrl bbi/GCF_000146045.2_R64.chainRBestGCF_000002945.1.bb
        linkDataUrl bbi/GCF_000146045.2_R64.chainRBestGCF_000002945.1Link.bb
        priority 3

    track mafNetGCF_000002945.1Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetGCF_000002945.1

        track netGCF_000002945.1
        parent mafNetGCF_000002945.1Viewnet
        subGroups view=net
        shortLabel brewer's yeast net
        longLabel brewer's yeast (2014-12-17) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_000146045.2_R64.GCF_000002945.1.net.bb
        summary bbi/GCF_000146045.2_R64.GCF_000002945.1.net.summary.bb
        speciesOrder GCF_000002945.1
        priority 4

        track synNetGCF_000002945.1
        parent mafNetGCF_000002945.1Viewnet
        subGroups view=net
        shortLabel brewer's yeast synNet
        longLabel brewer's yeast (2014-12-17) Syntenic Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_000146045.2_R64.GCF_000002945.1.synNet.bb
        summary bbi/GCF_000146045.2_R64.GCF_000002945.1.synNet.summary.bb
        speciesOrder GCF_000002945.1
        priority 5

        track rbestNetGCF_000002945.1
        parent mafNetGCF_000002945.1Viewnet
        subGroups view=net
        shortLabel brewer's yeast rbestNet
        longLabel brewer's yeast (2014-12-17) Reciprocal Best Net Alignment
        type bigMaf
        bigDataUrl bbi/GCF_000146045.2_R64.GCF_000002945.1.rbestNet.bb
        summary bbi/GCF_000146045.2_R64.GCF_000002945.1.rbestNet.summary.bb
        speciesOrder GCF_000002945.1
        priority 6


track VEuPathDBGeneModels
shortLabel VEuPathDB Genes
longLabel Gene Models mirrored from VEuPathDB
group genes
type bigBed 12 .
visibility pack
labelFields name
searchIndex name
bigDataUrl contrib/VEuPathDB/veupathGenes.bb
colorByStrand 0,0,122 157,60,32
dataVersion VEuPathDB release 68
html contrib/VEuPathDB/VEuPathDB

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 <b>Ref/Alt allele(s)</b>: $ref>$alt<br> <b>Var type</b>: $ucscClass<br> <b>AA change</b>: $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