083d201617a2e46b63f16cb8ee7d977fb5a7f0be hiram Wed Jun 18 15:00:42 2025 -0700 initial trackDb from GenArk refs #35898 diff --git src/hg/makeDb/trackDb/chicken/galGal7b/genArk.trackDb.ra src/hg/makeDb/trackDb/chicken/galGal7b/genArk.trackDb.ra new file mode 100644 index 00000000000..77ebdc49fab --- /dev/null +++ src/hg/makeDb/trackDb/chicken/galGal7b/genArk.trackDb.ra @@ -0,0 +1,896 @@ +track assembly +longLabel Assembly +shortLabel Assembly +visibility hide +colorByStrand 150,100,30 230,170,40 +color 150,100,30 +altColor 230,170,40 +bigDataUrl /gbdb/genark/GCF/016/699/485/GCF_016699485.2/bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.assembly.bb +type bigBed 6 +html /gbdb/genark/GCF/016/699/485/GCF_016699485.2/html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.assembly +searchIndex name +searchTrix /gbdb/genark/GCF/016/699/485/GCF_016699485.2/ixIxx/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.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 /gbdb/genark/GCF/016/699/485/GCF_016699485.2/bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.gap.bb +type bigBed 4 +group map +html /gbdb/genark/GCF/016/699/485/GCF_016699485.2/html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.gap + +track cytoBandIdeo +shortLabel Chromosome Band (Ideogram) +longLabel Ideogram for Orientation +group map +visibility dense +type bigBed 4 + +bigDataUrl /gbdb/genark/GCF/016/699/485/GCF_016699485.2/bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.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 /gbdb/genark/GCF/016/699/485/GCF_016699485.2/bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.gc5Base.bw +html /gbdb/genark/GCF/016/699/485/GCF_016699485.2/html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.gc5Base + +track tanDups +shortLabel Tandem Dups +longLabel Paired identical sequences +compositeTrack on +visibility hide +type bigBed 12 +group map +html /gbdb/genark/GCF/016/699/485/GCF_016699485.2/html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.tanDups + +track gapOverlap +parent tanDups on +shortLabel Gap Overlaps +longLabel Paired exactly identical sequence on each side of a gap +bigDataUrl /gbdb/genark/GCF/016/699/485/GCF_016699485.2/bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.gapOverlap.bb +type bigBed 12 + +track tandemDups +parent tanDups on +shortLabel Tandem Dups +longLabel Paired exactly identical sequence survey over entire genome assembly +bigDataUrl /gbdb/genark/GCF/016/699/485/GCF_016699485.2/bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.tandemDups.bb +type bigBed 12 + +track repeatMasker +shortLabel RepeatMasker +longLabel RepeatMasker Repetitive Elements +type bigRmsk 9 + +visibility pack +group varRep +bigDataUrl /gbdb/genark/GCF/016/699/485/GCF_016699485.2/bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.rmsk.bb +xrefDataUrl /gbdb/genark/GCF/016/699/485/GCF_016699485.2/bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.rmsk.align.bb +maxWindowToDraw 5000000 +html /gbdb/genark/GCF/016/699/485/GCF_016699485.2/html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.repeatMasker + +track repeatModeler +shortLabel RepeatModeler +longLabel RepeatModeler Repetitive Elements +type bigRmsk 9 + +visibility hide +group varRep +bigDataUrl /gbdb/genark/GCF/016/699/485/GCF_016699485.2/bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.rModel.bb +xrefDataUrl /gbdb/genark/GCF/016/699/485/GCF_016699485.2/bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.rModel.align.bb +maxWindowToDraw 5000000 +html /gbdb/genark/GCF/016/699/485/GCF_016699485.2/html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.repeatModeler + +track simpleRepeat +shortLabel Simple Repeats +longLabel Simple Tandem Repeats by TRF +group varRep +visibility dense +type bigBed 4 + +bigDataUrl /gbdb/genark/GCF/016/699/485/GCF_016699485.2/bbi/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.simpleRepeat.bb +html /gbdb/genark/GCF/016/699/485/GCF_016699485.2/html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.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 Gallus gallus Annotation Release 106 (2022-03-04) +html /gbdb/genark/GCF/016/699/485/GCF_016699485.2/html/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b.refSeqComposite +priority 2 + +track ncbiRefSeq +parent refSeqComposite on +color 12,12,120 +shortLabel RefSeq All +type bigGenePred +urls 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