hub GCA_000005575.1 genome assembly
shortLabel African malaria mosquito (PEST 2006)
longLabel African malaria mosquito (PEST 2006)/Anopheles gambiae str. PEST/GCA_000005575.1_AgamP3 genome assembly
useOneFile on
email genome-www@soe.ucsc.edu
descriptionUrl html/GCA_000005575.1_AgamP3.description.html

genome GCA_000005575.1
taxId 180454
groups groups.txt
description African malaria mosquito (PEST 2006)
twoBitPath GCA_000005575.1.2bit
twoBitBptUrl GCA_000005575.1.2bit.bpt
chromSizes GCA_000005575.1.chrom.sizes.txt
chromAliasBb GCA_000005575.1.chromAlias.bb
chromAuthority ucsc
organism AgamP3 Oct. 2006
defaultPos CM000357.1:20515035-20525035
scientificName Anopheles gambiae str. PEST
htmlPath html/GCA_000005575.1_AgamP3.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/000/005/575/GCA_000005575.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/000/005/575/GCA_000005575.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/000/005/575/GCA_000005575.1

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_000005575.1_AgamP3.assembly.bb
type bigBed 6
html html/GCA_000005575.1_AgamP3.assembly
searchIndex name
searchTrix ixIxx/GCA_000005575.1_AgamP3.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_000005575.1_AgamP3.gap.bb
type bigBed 4
group map
html html/GCA_000005575.1_AgamP3.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_000005575.1_AgamP3.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_000005575.1_AgamP3.gc5Base.bw
html html/GCA_000005575.1_AgamP3.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_000005575.1_AgamP3.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_000005575.1_AgamP3.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_000005575.1_AgamP3.tandemDups.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_000005575.1_AgamP3.rmsk.bb
maxWindowToDraw 5000000
html html/GCA_000005575.1_AgamP3.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_000005575.1_AgamP3.simpleRepeat.bb
html html/GCA_000005575.1_AgamP3.simpleRepeat

track ncbiGene
longLabel Gene models submitted to GenBank, ENA, DDBJ
shortLabel NCBI GenBank
visibility pack
color 0,80,150
altColor 150,80,0
colorByStrand 0,80,150 150,80,0
bigDataUrl bbi/GCA_000005575.1_AgamP3.ncbiGene.bb
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/$$"
html html/GCA_000005575.1_AgamP3.ncbiGene
searchIndex name
searchTrix ixIxx/GCA_000005575.1_AgamP3.ncbiGene.ix
urlLabel Entrez gene:
labelFields geneName,geneName2
defaultLabelFields geneName2
group genes

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_000005575.1_AgamP3.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_000005575.1_AgamP3.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_000005575.1_AgamP3.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_000005575.1_AgamP3.windowMasker.bb
html html/GCA_000005575.1_AgamP3.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_000005575.1_AgamP3.allGaps.bb
html html/GCA_000005575.1_AgamP3.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_000005575.1_AgamP3.augustus.bb
html html/GCA_000005575.1_AgamP3.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_000005575.1_AgamP3.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_000005575.1_AgamP3.xenoRefGene.ix
html html/GCA_000005575.1_AgamP3.xenoRefGene


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