track hubCentral compositeTrack on shortLabel my hub longLabel my hub group comphub subGroup1 view Track_Type Snake=Alignments subGroup2 orgs Organisms Anc0=Anc0 Pleuco=Pleuco mouse=mouse rn5=rn5 hg38=hg38 dragAndDrop subTracks #allButtonPair on dimensions dimensionX=view dimensionY=orgs noInherit on priority 0 centerLabelsDense on visibility full html ../documentation/hubCentral type bigBed 3 track hubCentralAlignments shortLabel Alignments view Alignments visibility full subTrack hubCentral track snakeAnc0 longLabel Anc0 shortLabel Anc0 otherSpecies Anc0 visibility full parent hubCentralAlignments showSnpWidth 2898 priority 2 bigDataUrl ../lod.txt type halSnake group snake subGroups view=Snake orgs=Anc0 track snakemouse longLabel mouse shortLabel mouse otherSpecies mouse visibility full parent hubCentralAlignments showSnpWidth 2898 priority 4 bigDataUrl ../lod.txt type halSnake group snake subGroups view=Snake orgs=mouse track snakern5 longLabel rn5 shortLabel rn5 otherSpecies rn5 visibility full parent hubCentralAlignments showSnpWidth 2898 priority 5 bigDataUrl ../lod.txt type halSnake group snake subGroups view=Snake orgs=rn5 track snakehg38 longLabel hg38 shortLabel hg38 otherSpecies hg38 visibility hide parent hubCentralAlignments off showSnpWidth 2898 priority 6 bigDataUrl ../lod.txt type halSnake group snake subGroups view=Snake orgs=hg38 track repeatMasker_ compositeTrack on shortLabel RepeatMasker longLabel Repeating Elements by RepeatMasker group varRep priority 149.1 visibility dense type bed 3 . noInherit on html ../trackDescriptions/repeatMasker track repeatMaskerSINE_ parent repeatMasker_ shortLabel SINE longLabel SINE Repeating Elements by RepeatMasker priority 1 spectrum on maxWindowToDraw 10000000 colorByStrand 50,50,150 150,50,50 type bigBed 6 + bigDataUrl RepeatMasker/peromyscus_assembly_scaffolds.rmsk.SINE.bb track repeatMaskerLINE_ parent repeatMasker_ shortLabel LINE longLabel LINE Repeating Elements by RepeatMasker priority 2 spectrum on maxWindowToDraw 10000000 colorByStrand 50,50,150 150,50,50 type bigBed 6 + bigDataUrl RepeatMasker/peromyscus_assembly_scaffolds.rmsk.LINE.bb track repeatMaskerLTR_ parent repeatMasker_ shortLabel LTR longLabel LTR Repeating Elements by RepeatMasker priority 3 spectrum on maxWindowToDraw 10000000 colorByStrand 50,50,150 150,50,50 type bigBed 6 + bigDataUrl RepeatMasker/peromyscus_assembly_scaffolds.rmsk.LTR.bb track repeatMaskerDNA_ parent repeatMasker_ shortLabel DNA longLabel DNA Repeating Elements by RepeatMasker priority 4 spectrum on maxWindowToDraw 10000000 colorByStrand 50,50,150 150,50,50 type bigBed 6 + bigDataUrl RepeatMasker/peromyscus_assembly_scaffolds.rmsk.DNA.bb track repeatMaskerSimple_ parent repeatMasker_ shortLabel Simple longLabel Simple Repeating Elements by RepeatMasker priority 5 spectrum on maxWindowToDraw 10000000 colorByStrand 50,50,150 150,50,50 type bigBed 6 + bigDataUrl RepeatMasker/peromyscus_assembly_scaffolds.rmsk.Simple.bb track repeatMaskerLowComplexity_ parent repeatMasker_ shortLabel Low Complexity longLabel Low Complexity Repeating Elements by RepeatMasker priority 6 spectrum on maxWindowToDraw 10000000 colorByStrand 50,50,150 150,50,50 type bigBed 6 + bigDataUrl RepeatMasker/peromyscus_assembly_scaffolds.rmsk.Low_complexity.bb track repeatMaskerSatellite_ parent repeatMasker_ shortLabel Satellite longLabel Satellite Repeating Elements by RepeatMasker priority 7 spectrum on maxWindowToDraw 10000000 colorByStrand 50,50,150 150,50,50 type bigBed 6 + bigDataUrl RepeatMasker/peromyscus_assembly_scaffolds.rmsk.Satellite.bb track repeatMaskerUnknown_ parent repeatMasker_ shortLabel RNA longLabel RNA Repeating Elements by RepeatMasker priority 8 spectrum on maxWindowToDraw 10000000 colorByStrand 50,50,150 150,50,50 type bigBed 6 + bigDataUrl RepeatMasker/peromyscus_assembly_scaffolds.rmsk.Unknown.bb track genes_ compositeTrack on shortLabel Genes longLabel Genes and Gene liftovers group genes priority 149.1 visibility dense type bed 3 . noInherit on html ../trackDescriptions/genes track genesh38_ parent genes_ shortLabel h38 longLabel human to P. leucopus priority 5 spectrum on maxWindowToDraw 10000000 colorByStrand 50,50,150 150,50,50 type bigBed 12 + searchIndex name bigDataUrl Genes/h38_2_Pleuco_genes.bigBed track genesm38_ parent genes_ shortLabel m38 longLabel mouse to P. leucopus priority 6 spectrum on maxWindowToDraw 10000000 colorByStrand 50,50,150 150,50,50 type bigBed 12 + bigDataUrl Genes/m38_2_Pleuco_genes.bigBed track genesrn5_ parent genes_ shortLabel rn5 longLabel rat to P. leucopus priority 7 spectrum on maxWindowToDraw 10000000 colorByStrand 50,50,150 150,50,50 type bigBed 12 + bigDataUrl Genes/rn5_2_Pleuco_genes.bigBed track genesPleuco_ parent genes_ shortLabel Pleuco longLabel P. leucopus Augustus annotation priority 1 spectrum on maxWindowToDraw 10000000 colorByStrand 50,50,150 150,50,50 type bigBed 12 + searchIndex name bigDataUrl Genes/Pleuco_genes.bigBed track genesh38Exonerate_ parent genes_ shortLabel h38Exonerate longLabel human proteins to P leucopus using exonerate priority 3 spectrum on maxWindowToDraw 10000000 colorByStrand 50,50,150 150,50,50 type bigBed 12 + searchIndex name bigDataUrl Genes/exonerate.hum2Pleuc.bigBed searchTrix Genes/exonerate.hum2Pleuc.search.ix labelFields name2 track genesmusExonerate_ parent genes_ shortLabel mouseExonerate longLabel mouse uniprot-AUP000000589 proteins to P leucopus using exonerate priority 4 spectrum on maxWindowToDraw 10000000 colorByStrand 50,50,150 150,50,50 type bigBed 12 + searchIndex name bigDataUrl Genes/exonerate.mus2Pleuc.bigBed track genesPleucostraw_ parent genes_ shortLabel PleucoStrawberry longLabel P. leucopus gene predictions from RNAseq, hisat2, strawberry priority 2 spectrum on maxWindowToDraw 10000000 colorByStrand 50,50,150 150,50,50 type bigBed 12 + searchIndex name bigDataUrl Genes/Pleuc.strawberry.bigBed track Pero_0.1_gene_annotation_ parent genes_ shortLabel Pero_0.1 longLabel P leucopus reference gene annotation from Genbank 0.1 priority 3 spectrum on maxWindowToDraw 10000000 colorByStrand 50,50,150 150,50,50 type bigBed 12 + searchIndex name bigDataUrl Genes/ref_Pero_0.1.bigBed searchTrix Genes/ref_Pero_0.1.search.ix labelFields name2 track alignability bigDataUrl Pleuco.alignability.bw shortLabel Alignability longLabel Alignability from Progressive Cactus type bigWig track Variation compositeTrack on shortLabel Variation longLabel SNPs, INDELs, CNVs in P. leucopus priority 0 centerLabelsDense on type vcfTabix html ../documentation/hubCentral track CNVs parent Variation on priority 1 bigDataUrl Variation/CNV.vcf.gz shortLabel exonic P. leucopus CNVs longLabel exonic CNVs identified in three high coverage samples visibility dense type vcfTabix track High_SNPs parent Variation on priority 2 bigDataUrl Variation/High_hE.vcf.gz shortLabel P. leucopus High Effect longLabel High Effect SNPs identified from human exonerate gene model visibility dense type vcfTabix track Moderate_SNPs parent Variation on priority 3 bigDataUrl Variation/Moderate_hE.vcf.gz shortLabel P. leucopus Moderate Effect longLabel Moderate Effect SNPs identified from human exonerate gene model visibility dense type vcfTabix track Low_SNPs parent Variation on priority 4 bigDataUrl Variation/Low_hE.vcf.gz shortLabel P. leucopus Low Effect longLabel Low Effect SNPs identified from human exonerate gene model visibility dense type vcfTabix track Other_SNPs parent Variation on priority 5 bigDataUrl Variation/AllOthers_hE.vcf.gz shortLabel P. leucopus Other SNPs longLabel "Modifier" [/ All Other] SNPs identified from human exonerate gene model visibility dense type vcfTabix