hub GCA_949553875.1 genome assembly
shortLabel E. coli (K-12 MG1655 2023)
longLabel E. coli (K-12 MG1655 2023)/Escherichia coli str. K-12 substr. MG1655/GCA_949553875.1_sample2_Strain154_Phi80.fasta genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCA_949553875.1_sample2_Strain154_Phi80.fasta.description.html

genome GCA_949553875.1
taxId 511145
groups groups.txt
description E. coli (K-12 MG1655 2023)
twoBitPath GCA_949553875.1.2bit
twoBitBptUrl GCA_949553875.1.2bit.bpt
chromSizes GCA_949553875.1.chrom.sizes.txt
chromAliasBb GCA_949553875.1.chromAlias.bb
organism sample2_Strain154_Phi80.fasta Jun. 2023
defaultPos CATIQD010000001.1:884405-894405
scientificName Escherichia coli str. K-12 substr. MG1655
htmlPath html/GCA_949553875.1_sample2_Strain154_Phi80.fasta.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/949/553/875/GCA_949553875.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/949/553/875/GCA_949553875.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/949/553/875/GCA_949553875.1

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_949553875.1_sample2_Strain154_Phi80.fasta.assembly.bb
type bigBed 6
html html/GCA_949553875.1_sample2_Strain154_Phi80.fasta.assembly
searchIndex name
searchTrix ixIxx/GCA_949553875.1_sample2_Strain154_Phi80.fasta.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_949553875.1_sample2_Strain154_Phi80.fasta.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_949553875.1_sample2_Strain154_Phi80.fasta.gc5Base.bw
html html/GCA_949553875.1_sample2_Strain154_Phi80.fasta.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_949553875.1_sample2_Strain154_Phi80.fasta.tanDups

    track tandemDups
    parent tanDups on
    shortLabel Tandem Dups
    longLabel Paired exactly identical sequence survey over entire genome assembly
    bigDataUrl bbi/GCA_949553875.1_sample2_Strain154_Phi80.fasta.tandemDups.bb
    type bigBed 12

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_949553875.1_sample2_Strain154_Phi80.fasta.simpleRepeat.bb
html html/GCA_949553875.1_sample2_Strain154_Phi80.fasta.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_949553875.1_sample2_Strain154_Phi80.fasta.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_949553875.1_sample2_Strain154_Phi80.fasta.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_949553875.1_sample2_Strain154_Phi80.fasta.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_949553875.1_sample2_Strain154_Phi80.fasta.windowMasker.bb
html html/GCA_949553875.1_sample2_Strain154_Phi80.fasta.windowMasker