hub mpxvRivers genome assembly
shortLabel MPXV-M5312_HM12_Rivers (MT903340.1/GCF_014621545.1)
longLabel Monkeypox virus
email genome-www@soe.ucsc.edu
desriptionUrl /gbdb/mpxvRivers/html/description.html
useOneFile on

genome mpxvRivers
taxId 10244
groups ../groups.txt
description MPXV-M5312_HM12_Rivers (MT903340.1/GCF_014621545.1)
twoBitPath /gbdb/mpxvRivers/mpxvRivers.2bit
chromAliasBb /gbdb/mpxvRivers/hubs/chromAlias.bb
chromSizes /gbdb/mpxvRivers/hubs/chromSizes.txt
organism Monkeypox virus
defaultPos NC_063383.1:65,736-75,736
scientificName Monkeypox virus
htmlPath /gbdb/mpxvRivers/html/description.html
blat dynablat-01 4040 dynamic mpxvRivers
isPcr dynablat-01 4040 dynamic mpxvRivers
transBlat dynablat-01 4040 dynamic mpxvRivers

track viralzoneGenes
type bigBed 9 +
html viralzoneGenes.html
visibility pack
shortLabel Viralzone Transcriptome
group genes
priority 10
itemRgb on
bigDataUrl /gbdb/mpxvRivers/viralzoneGenes/viralzone.bb
longLabel Viralzone Transcriptome: early=green, intermediate=bleu, late=red
mouseOverField stage

track assembly
type bigBed 6
html assembly.html
colorByStrand 150,100,30 230,170,40
visibility pack
shortLabel Assembly
group map
searchIndex name
searchTrix /gbdb/mpxvRivers/ixIxx/GCF_014621545.1_ASM1462154v1.assembly.ix
bigDataUrl /gbdb/mpxvRivers/bbi/GCF_014621545.1_ASM1462154v1.assembly.bb
altColor 230,170,40
color 150,100,30
urlLabel NCBI Nucleotide database
longLabel Assembly
url https://www.ncbi.nlm.nih.gov/nuccore/$$

track cytoBandIdeo
type bigBed 4 +
visibility dense
shortLabel Chromosome Band (Ideogram)
group map
bigDataUrl /gbdb/mpxvRivers/bbi/GCF_014621545.1_ASM1462154v1.cytoBand.bb
longLabel Ideogram for Orientation

track gc5Base
type bigWig 0 100
html gc5Base.html
visibility full
shortLabel GC Percent
windowingFunction Mean
maxHeightPixels 128:36:16
group map
gridDefault OFF
graphTypeDefault Bar
bigDataUrl /gbdb/mpxvRivers/bbi/GCF_014621545.1_ASM1462154v1.gc5Base.bw
altColor 128,128,128
color 0,0,0
autoScale Off
viewLimits 30:70
longLabel GC Percent in 5-Base Windows

track genbankAli
type bigPsl
html genbankAli.html
visibility squish
shortLabel Genbank Alignments
group map
bigDataUrl /gbdb/mpxvRivers/genbankAli/seqs.bb
color 150,100,30
longLabel Genbank Alignments: alignments of sequences in Genbank to the reference

track ncbiGene
type bigGenePred
html ncbiGene.html
visibility pack
shortLabel NCBI Genes
group genes
searchIndex name
labelFields geneName,geneName2
searchTrix /gbdb/mpxvRivers/ixIxx/GCF_014621545.1_ASM1462154v1.ncbiGene.ix
bigDataUrl /gbdb/mpxvRivers/bbi/GCF_014621545.1_ASM1462154v1.ncbiGene.bb
altColor 150,80,0
color 0,80,150
urlLabel Entrez gene
defaultLabelFields geneName2
longLabel NCBI gene predictions
url https://www.ncbi.nlm.nih.gov/gene/?term=$$

track pcrAmplicon
type bigBed 12 +
html pcrAmplicon.html
visibility dense
shortLabel PCR Sequencing
group map
compositeTrack on
longLabel PCR Sequencing Protocols: Amplicons and Primers

track pcrWelkers
type bigBed 12 +
html pcrWelkers.html
visibility dense
shortLabel Welkers et al
group map
bigDataUrl /gbdb/mpxvRivers/pcrAmplicon/pcrWelkers.bb
parent pcrAmplicon on
noScoreFilter on
longLabel PCR Amplicons: Welkers et al. 2022 V1

track pcrChen
type bigBed 12 +
html pcrChen.html
visibility dense
shortLabel Yale hMPXV
group map
bigDataUrl /gbdb/mpxvRivers/pcrAmplicon/pcrAmplicon.bb
parent pcrAmplicon on
noScoreFilter on
longLabel PCR Amplicons: Yale hMPXV Amplicon Scheme (Chen et al. 2022 V2)

track simpleRepeat
type bigBed 4 +
html simpleRepeat.html
visibility dense
shortLabel Simple Repeats
group varRep
bigDataUrl /gbdb/mpxvRivers/bbi/GCF_014621545.1_ASM1462154v1.simpleRepeat.bb
longLabel Simple Tandem Repeats by TRF

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

track tandemDups
type bigBed 12
html tandemDups.html
shortLabel Tandem Dups
bigDataUrl /gbdb/mpxvRivers/bbi/GCF_014621545.1_ASM1462154v1.tandemDups.bb
parent tanDups on
longLabel Paired exactly identical sequence survey over entire genome assembly

track windowMasker
type bigBed 3
html windowMasker.html
visibility dense
shortLabel WM + SDust
group varRep
bigDataUrl /gbdb/mpxvRivers/bbi/GCF_014621545.1_ASM1462154v1.windowMasker.bb
longLabel Genomic Intervals Masked by WindowMasker + SDust