hub GCA_964261385.2 genome assembly
shortLabel common newt (v2 alternate hap 2026)
longLabel common newt (v2 alternate hap 2026)/Lissotriton vulgaris/GCA_964261385.2_aLisVul1.2_alternate_haplotype genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCA_964261385.2_aLisVul1.2_alternate_haplotype.description.html

genome GCA_964261385.2
taxId 8324
groups groups.txt
description common newt (v2 alternate hap 2026)
twoBitPath GCA_964261385.2.2bit
twoBitBptUrl GCA_964261385.2.2bit.bpt
chromSizes GCA_964261385.2.chrom.sizes.txt
chromAliasBb GCA_964261385.2.chromAlias.bb
organism aLisVul1.2_alternate_haplotype Apr. 2026
defaultPos CAXVPM020191156.1:8307684-8317684
scientificName Lissotriton vulgaris
htmlPath html/GCA_964261385.2_aLisVul1.2_alternate_haplotype.description.html
blat dynablat-01.soe.ucsc.edu 4041 dynamic GCA/964/261/385/GCA_964261385.2
transBlat dynablat-01.soe.ucsc.edu 4041 dynamic GCA/964/261/385/GCA_964261385.2
isPcr dynablat-01.soe.ucsc.edu 4041 dynamic GCA/964/261/385/GCA_964261385.2

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_964261385.2_aLisVul1.2_alternate_haplotype.assembly.bb
type bigBed 6
html html/GCA_964261385.2_aLisVul1.2_alternate_haplotype.assembly
searchIndex name
searchTrix ixIxx/GCA_964261385.2_aLisVul1.2_alternate_haplotype.assembly.ix
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_964261385.2_aLisVul1.2_alternate_haplotype.gap.bb
type bigBed 4
group map
html html/GCA_964261385.2_aLisVul1.2_alternate_haplotype.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_964261385.2_aLisVul1.2_alternate_haplotype.cytoBand.bb

# gcOnFly is a synthetic track, computed at run time
# this trackDb entry will allow it to operate properly with
# correct visibility when a saved session is restored
track gcOnFly
shortLabel GC Percent
longLabel GC Percent in 5-Base Windows
group map
visibility dense
type bigWig 0 100
bigDataUrl bbi/GCA_964261385.2_aLisVul1.2_alternate_haplotype.gcOnFly.bw
gcOnFlyMaxDensity 50000
syntheticTrack on
calcWinSize 5
autoScale Off
viewLimits 30:70
maxHeightPixels 128:36:16
graphTypeDefault Bar
gridDefault OFF
windowingFunction Mean
color 0,0,0
altColor 128,128,128
html html/GCA_964261385.2_aLisVul1.2_alternate_haplotype.gcOnFly

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_964261385.2_aLisVul1.2_alternate_haplotype.rmsk.bb
xrefDataUrl bbi/GCA_964261385.2_aLisVul1.2_alternate_haplotype.rmsk.align.bb
maxWindowToDraw 5000000
html html/GCA_964261385.2_aLisVul1.2_alternate_haplotype.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_964261385.2_aLisVul1.2_alternate_haplotype.simpleRepeat.bb
html html/GCA_964261385.2_aLisVul1.2_alternate_haplotype.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_964261385.2_aLisVul1.2_alternate_haplotype.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_964261385.2_aLisVul1.2_alternate_haplotype.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_964261385.2_aLisVul1.2_alternate_haplotype.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_964261385.2_aLisVul1.2_alternate_haplotype.windowMasker.bb
html html/GCA_964261385.2_aLisVul1.2_alternate_haplotype.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_964261385.2_aLisVul1.2_alternate_haplotype.allGaps.bb
html html/GCA_964261385.2_aLisVul1.2_alternate_haplotype.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_964261385.2_aLisVul1.2_alternate_haplotype.augustus.bb
html html/GCA_964261385.2_aLisVul1.2_alternate_haplotype.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_964261385.2_aLisVul1.2_alternate_haplotype.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_964261385.2_aLisVul1.2_alternate_haplotype.xenoRefGene.ix
html html/GCA_964261385.2_aLisVul1.2_alternate_haplotype.xenoRefGene