track assembly
longLabel Assembly
shortLabel Assembly
visibility pack
colorByStrand 150,100,30 230,170,40
color 150,100,30
altColor 230,170,40
bigDataUrl bbi/GCA_902500255.1_fThaAma1.1.assembly.bb
type bigBed 6
html html/GCA_902500255.1_fThaAma1.1.assembly
searchIndex name
searchTrix ixIxx/GCA_902500255.1_fThaAma1.1.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/GCA_902500255.1_fThaAma1.1.cytoBand.bb
track gc5Base
shortLabel GC Percent
longLabel GC Percent in 5-Base Windows
group map
visibility full
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_902500255.1_fThaAma1.1.gc5Base.bw
html html/GCA_902500255.1_fThaAma1.1.gc5Base
track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_902500255.1_fThaAma1.1.tanDups
track gapOverlap
parent tanDups on
shortLabel Gap Overlaps
longLabel Paired exactly identical sequence on each side of a gap
bigDataUrl bbi/GCA_902500255.1_fThaAma1.1.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_902500255.1_fThaAma1.1.tandemDups.bb
type bigBed 12
track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_902500255.1_fThaAma1.1.rmsk.bb
maxWindowToDraw 5000000
html html/GCA_902500255.1_fThaAma1.1.repeatMasker
track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_902500255.1_fThaAma1.1.simpleRepeat.bb
html html/GCA_902500255.1_fThaAma1.1.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 NCBI Thalassophryne amazonica Annotation Release 100 (2020-05-09)
html html/GCA_902500255.1_fThaAma1.1.refSeqComposite
priority 2
track ncbiRefSeq
parent refSeqComposite on
color 12,12,120
altColor 120,12,12
shortLabel RefSeq All
type bigGenePred
labelFields name,geneName,geneName2
defaultLabelFields geneName2
searchIndex name
searchTrix ixIxx/GCA_902500255.1_fThaAma1.1.ncbiRefSeq.ix
bigDataUrl bbi/GCA_902500255.1_fThaAma1.1.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 ncbiRefSeqPredicted
color 12,12,120
parent refSeqComposite on
shortLabel RefSeq Predicted
longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*)
type bigGenePred
labelFields name,geneName,geneName2
defaultLabelFields geneName2
searchIndex name
searchTrix ixIxx/GCA_902500255.1_fThaAma1.1.ncbiRefSeqPredicted.ix
idXref ncbiRefSeqLink mrnaAcc name
bigDataUrl bbi/GCA_902500255.1_fThaAma1.1.ncbiRefSeqPredicted.bb
baseColorUseCds given
baseColorDefault genomicCodons
priority 3
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/GCA_902500255.1_fThaAma1.1.ncbiRefSeqOther.ix
bigDataUrl bbi/GCA_902500255.1_fThaAma1.1.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/GCA_902500255.1_fThaAma1.1.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 pack
type bigBed 4 +
html html/GCA_902500255.1_fThaAma1.1.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_902500255.1_fThaAma1.1.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_902500255.1_fThaAma1.1.cpgIslandExtUnmasked.bb
track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_902500255.1_fThaAma1.1.windowMasker.bb
html html/GCA_902500255.1_fThaAma1.1.windowMasker
track allGaps
shortLabel All Gaps
longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps
group map
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_902500255.1_fThaAma1.1.allGaps.bb
html html/GCA_902500255.1_fThaAma1.1.allGaps
track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_902500255.1_fThaAma1.1.augustus.bb
html html/GCA_902500255.1_fThaAma1.1.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_902500255.1_fThaAma1.1.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_902500255.1_fThaAma1.1.xenoRefGene.ix
html html/GCA_902500255.1_fThaAma1.1.xenoRefGene
track ensGene
shortLabel Ensembl genes
longLabel Ensembl genes 2020_05
group genes
priority 40
visibility pack
color 150,0,0
itemRgb on
type bigGenePred
bigDataUrl bbi/GCA_902500255.1_fThaAma1.1.ensGene.bb
searchTrix ixIxx/GCA_902500255.1_fThaAma1.1.ensGene.ix
searchIndex name
labelFields name,name2
defaultLabelFields name2
baseColorUseCds given
baseColorDefault genomicCodons
labelSeperator " "
html html/GCA_902500255.1_fThaAma1.1.ensGene