c44506b985f933067aed6688d2470dd7d577833c
markd
  Thu Apr 14 12:20:08 2022 -0700
use hubCheck -checkSettings and remove invalid settings

diff --git src/hg/makeDb/doc/chm13v2.0/hub.txt src/hg/makeDb/doc/chm13v2.0/hub.txt
index dd8f26c..b61a0a0 100644
--- src/hg/makeDb/doc/chm13v2.0/hub.txt
+++ src/hg/makeDb/doc/chm13v2.0/hub.txt
@@ -1,618 +1,616 @@
 hub GCA_009914755.4 genome assembly
-shortLabel human T2T CHM13 v2.0
-longLabel human T2T CHM13 v2.0/Homo sapiens/GCA_009914755.4_T2T-CHM13v2.0 genome assembly
+shortLabel human T2T-CHM13 v2.0
+longLabel human T2T-CHM13 v2.0/Homo sapiens/GCA_009914755.4_T2T-CHM13v2.0 genome assembly
 email hclawson@ucsc.edu
 descriptionUrl html/GCA_009914755.4_T2T-CHM13v2.0.description.html
 useOneFile on
 
 genome GCA_009914755.4
 taxId 9606
 groups groups.txt
-description human T2T CHM13 v2.0
+description human T2T-CHM13 v2.0
 twoBitPath GCA_009914755.4.2bit
 twoBitBptUrl GCA_009914755.4.2bit.bpt
 chromSizes GCA_009914755.4.chrom.sizes.txt
 chromAlias GCA_009914755.4.chromAlias.txt
-organism human T2T CHM13 v2.0
-defaultPos CP068269.2:145462284-145491793
+organism human T2T-CHM13 v2.0
+defaultPos CP068269.2:145458455-145495201
 scientificName Homo sapiens
 htmlPath html/GCA_009914755.4_T2T-CHM13v2.0.description.html
 blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/009/914/755/GCA_009914755.4
 transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/009/914/755/GCA_009914755.4
 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/009/914/755/GCA_009914755.4
 liftOver.GCA_021950905.1 liftOver/GCA_009914755.4ToGCA_021950905.1.over.chain.gz
 liftOver.GCA_021951015.1 liftOver/GCA_009914755.4ToGCA_021951015.1.over.chain.gz
 liftOver.hg19 liftOver/GCA_009914755.4ToHg19.over.chain.gz
 liftOver.hg38 liftOver/GCA_009914755.4ToHg38.over.chain.gz
 
 track assembly
-longLabel Assembly
+longLabel Assembly from NCBI Genbank Sequences
 shortLabel Assembly
-visibility pack
+visibility hide
 colorByStrand 150,100,30 230,170,40
 color 150,100,30
 altColor 230,170,40
 bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.assembly.bb
 type bigBed 6
 html html/GCA_009914755.4_T2T-CHM13v2.0.assembly
 searchIndex name
 searchTrix ixIxx/GCA_009914755.4_T2T-CHM13v2.0.assembly.ix
 url https://www.ncbi.nlm.nih.gov/nuccore/$$
 urlLabel NCBI Nucleotide database
 group map
 
 track gc5Base
 shortLabel GC Percent
 longLabel GC Percent in 5-Base Windows
 group map
-visibility full
+visibility hide
 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_009914755.4_T2T-CHM13v2.0.gc5Base.bw
 html html/GCA_009914755.4_T2T-CHM13v2.0.gc5Base
 
 track repeatMasker
 compositeTrack on
 shortLabel RepeatMasker
 longLabel Repeating Elements by RepeatMasker
 group varRep
-visibility dense
+visibility hide
 type bigBed 6 +
 colorByStrand 50,50,150 150,50,50
 maxWindowToDraw 10000000
 spectrum on
 html html/GCA_009914755.4_T2T-CHM13v2.0.repeatMasker
 
     track repeatMaskerSINE
     parent repeatMasker
     shortLabel SINE
     longLabel SINE Repeating Elements by RepeatMasker
     type bigBed 6 +
     priority 1
     bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.rmsk.SINE.bb
 
     track repeatMaskerLINE
     parent repeatMasker
     shortLabel LINE
     longLabel LINE Repeating Elements by RepeatMasker
     type bigBed 6 +
     priority 2
     bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.rmsk.LINE.bb
 
     track repeatMaskerLTR
     parent repeatMasker
     shortLabel LTR
     longLabel LTR Repeating Elements by RepeatMasker
     type bigBed 6 +
     priority 3
     bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.rmsk.LTR.bb
 
     track repeatMaskerDNA
     parent repeatMasker
     shortLabel DNA
     longLabel DNA Repeating Elements by RepeatMasker
     type bigBed 6 +
     priority 4
     bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.rmsk.DNA.bb
 
     track repeatMaskerSimple
     parent repeatMasker
     shortLabel Simple
     longLabel Simple Repeating Elements by RepeatMasker
     type bigBed 6 +
     priority 5
     bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.rmsk.Simple.bb
 
     track repeatMaskerLowComplexity
     parent repeatMasker
     shortLabel Low Complexity
     longLabel Low Complexity Repeating Elements by RepeatMasker
     type bigBed 6 +
     priority 6
     bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.rmsk.Low_complexity.bb
 
     track repeatMaskerSatellite
     parent repeatMasker
     shortLabel Satellite
     longLabel Satellite Repeating Elements by RepeatMasker
     type bigBed 6 +
     priority 7
     bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.rmsk.Satellite.bb
 
     track repeatMaskerRNA
     parent repeatMasker
     shortLabel RNA
     longLabel RNA Repeating Elements by RepeatMasker
     type bigBed 6 +
     priority 8
     bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.rmsk.RNA.bb
 
     track repeatMaskerOther
     parent repeatMasker
     shortLabel Other
     longLabel Other Repeating Elements by RepeatMasker
     type bigBed 6 +
     priority 9
     bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.rmsk.Other.bb
 
 track simpleRepeat
 shortLabel Simple Repeats
 longLabel Simple Tandem Repeats by TRF
 group varRep
-visibility dense
+visibility hide
 type bigBed 4 +
 bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.simpleRepeat.bb
 html html/GCA_009914755.4_T2T-CHM13v2.0.simpleRepeat
 
 track cpgIslands
 compositeTrack on
 shortLabel CpG Islands
 longLabel CpG Islands (Islands < 300 Bases are Light Green)
 group regulation
-visibility pack
+visibility hide
 type bigBed 4 +
 html html/GCA_009914755.4_T2T-CHM13v2.0.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_009914755.4_T2T-CHM13v2.0.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_009914755.4_T2T-CHM13v2.0.cpgIslandExtUnmasked.bb
 
 track windowMasker
 shortLabel WM + SDust
 longLabel Genomic Intervals Masked by WindowMasker + SDust
 group varRep
-visibility dense
+visibility hide
 type bigBed 3
 bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.windowMasker.bb
 html html/GCA_009914755.4_T2T-CHM13v2.0.windowMasker
 
 track xenoRefGene
 shortLabel RefSeq mRNAs
 longLabel RefSeq mRNAs mapped to this assembly
 group rna
-visibility pack
+visibility hide
 color 180,0,0
 type bigGenePred
 bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.xenoRefGene.bb
 labelFields name,geneName,geneName2
 searchIndex name
 searchTrix ixIxx/GCA_009914755.4_T2T-CHM13v2.0.xenoRefGene.ix
 html html/GCA_009914755.4_T2T-CHM13v2.0.xenoRefGene
 
 track GCA_009914755.4_T2T-CHM13v2.0ChainNet
 compositeTrack on
-shortLabel Chain/Net
+shortLabel Human Chain/Net
 longLabel Chain and Net alignments to target sequence: GCA_009914755.4_T2T-CHM13v2.0
 subGroup1 view Views chain=Chains net=Nets
 subGroup2 species Species s000=GCA_021950905.1 s001=GCA_021951015.1 s002=hg19 s003=hg38
 subGroup3 clade Clade c00=human
 dragAndDrop subTracks
-visibility hide
+visibility full
 group compGeno
 color 0,0,0
 altColor 255,255,0
 type bed 3
-chainLinearGap loose
-chainMinScore 5000
 dimensions dimensionX=clade dimensionY=species
 sortOrder species=+ view=+ clade=+
 configurable on
 html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
 
     track GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain
     shortLabel  Chains
     view chain
     visibility pack
     subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNet
     spectrum on
 
         track chainGCA_021950905.1
         subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off
         subGroups view=chain species=s000 clade=c00
-        shortLabel GCA_021950905.1 Chain
-        longLabel GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Chained Alignments
+        shortLabel HG002 pat Chain
+        longLabel HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Chained Alignments
         type bigChain GCA_021950905.1
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainGCA_021950905.1.bb
         linkDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainGCA_021950905.1Link.bb
         otherDb GCA_021950905.1
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 1
 
         track chainSynGCA_021950905.1
         subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off
         subGroups view=chain species=s000 clade=c00
-        shortLabel GCA_021950905.1 synChain
-        longLabel GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Syntenic Chained Alignments
+        shortLabel HG002 pat synChain
+        longLabel HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Syntenic Chained Alignments
         type bigChain GCA_021950905.1
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainSynGCA_021950905.1.bb
         linkDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainSynGCA_021950905.1Link.bb
         otherDb GCA_021950905.1
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 2
 
         track chainRBestGCA_021950905.1
         subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off
         subGroups view=chain species=s000 clade=c00
-        shortLabel GCA_021950905.1 rbChain
-        longLabel GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Reciprocal Best Chained Alignments
+        shortLabel HG002 pat rbChain
+        longLabel HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Reciprocal Best Chained Alignments
         type bigChain GCA_021950905.1
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainRBestGCA_021950905.1.bb
         linkDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainRBestGCA_021950905.1Link.bb
         otherDb GCA_021950905.1
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 3
 
         track chainLiftOverGCA_021950905.1
         subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off
         subGroups view=chain species=s000 clade=c00
-        shortLabel GCA_021950905.1 loChain
-        longLabel GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Lift Over Chained Alignments
+        shortLabel HG002 pat loChain
+        longLabel HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Lift Over Chained Alignments
         type bigChain GCA_021950905.1
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainLiftOverGCA_021950905.1.bb
         linkDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainLiftOverGCA_021950905.1Link.bb
         otherDb GCA_021950905.1
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 4
 
         track chainGCA_021951015.1
         subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off
         subGroups view=chain species=s001 clade=c00
-        shortLabel GCA_021951015.1 Chain
-        longLabel GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Chained Alignments
+        shortLabel HG002 mat Chain
+        longLabel HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Chained Alignments
         type bigChain GCA_021951015.1
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainGCA_021951015.1.bb
         linkDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainGCA_021951015.1Link.bb
         otherDb GCA_021951015.1
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 5
 
         track chainSynGCA_021951015.1
         subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off
         subGroups view=chain species=s001 clade=c00
-        shortLabel GCA_021951015.1 synChain
-        longLabel GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Syntenic Chained Alignments
+        shortLabel HG002 mat synChain
+        longLabel HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Syntenic Chained Alignments
         type bigChain GCA_021951015.1
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainSynGCA_021951015.1.bb
         linkDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainSynGCA_021951015.1Link.bb
         otherDb GCA_021951015.1
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 6
 
         track chainRBestGCA_021951015.1
         subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off
         subGroups view=chain species=s001 clade=c00
-        shortLabel GCA_021951015.1 rbChain
-        longLabel GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Reciprocal Best Chained Alignments
+        shortLabel HG002 mat rbChain
+        longLabel HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Reciprocal Best Chained Alignments
         type bigChain GCA_021951015.1
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainRBestGCA_021951015.1.bb
         linkDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainRBestGCA_021951015.1Link.bb
         otherDb GCA_021951015.1
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 7
 
         track chainLiftOverGCA_021951015.1
         subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off
         subGroups view=chain species=s001 clade=c00
-        shortLabel GCA_021951015.1 loChain
-        longLabel GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Lift Over Chained Alignments
+        shortLabel HG002 mat loChain
+        longLabel HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Lift Over Chained Alignments
         type bigChain GCA_021951015.1
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainLiftOverGCA_021951015.1.bb
         linkDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainLiftOverGCA_021951015.1Link.bb
         otherDb GCA_021951015.1
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 8
 
         track chainHg19
         subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off
         subGroups view=chain species=s002 clade=c00
         shortLabel hg19 Chain
         longLabel hg19 (Feb. 2009) Chained Alignments
         type bigChain hg19
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainHg19.bb
         linkDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainHg19Link.bb
         otherDb hg19
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 9
 
         track chainSynHg19
         subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off
         subGroups view=chain species=s002 clade=c00
         shortLabel hg19 synChain
         longLabel hg19 (Feb. 2009) Syntenic Chained Alignments
         type bigChain hg19
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainSynHg19.bb
         linkDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainSynHg19Link.bb
         otherDb hg19
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 10
 
         track chainRBestHg19
         subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off
         subGroups view=chain species=s002 clade=c00
         shortLabel hg19 rbChain
         longLabel hg19 (Feb. 2009) Reciprocal Best Chained Alignments
         type bigChain hg19
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainRBestHg19.bb
         linkDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainRBestHg19Link.bb
         otherDb hg19
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 11
 
         track chainLiftOverHg19
         subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off
         subGroups view=chain species=s002 clade=c00
         shortLabel hg19 loChain
         longLabel hg19 (Feb. 2009) Lift Over Chained Alignments
         type bigChain hg19
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainLiftOverHg19.bb
         linkDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainLiftOverHg19Link.bb
         otherDb hg19
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 12
 
         track chainHg38
         subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off
         subGroups view=chain species=s003 clade=c00
         shortLabel hg38 Chain
         longLabel hg38 (Dec. 2013) Chained Alignments
         type bigChain hg38
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainHg38.bb
         linkDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainHg38Link.bb
         otherDb hg38
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 13
 
         track chainSynHg38
         subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off
         subGroups view=chain species=s003 clade=c00
         shortLabel hg38 synChain
         longLabel hg38 (Dec. 2013) Syntenic Chained Alignments
         type bigChain hg38
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainSynHg38.bb
         linkDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainSynHg38Link.bb
         otherDb hg38
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 14
 
         track chainRBestHg38
         subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off
         subGroups view=chain species=s003 clade=c00
         shortLabel hg38 rbChain
         longLabel hg38 (Dec. 2013) Reciprocal Best Chained Alignments
         type bigChain hg38
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainRBestHg38.bb
         linkDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainRBestHg38Link.bb
         otherDb hg38
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 15
 
         track chainLiftOverHg38
-        subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off
+        subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain on
         subGroups view=chain species=s003 clade=c00
         shortLabel hg38 loChain
         longLabel hg38 (Dec. 2013) Lift Over Chained Alignments
         type bigChain hg38
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainLiftOverHg38.bb
         linkDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainLiftOverHg38Link.bb
         otherDb hg38
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 16
 
     track GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
     shortLabel Nets
     view net
-    visibility dense
+    visibility hide
     subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNet
 
         track netGCA_021950905.1
         parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
         subGroups view=net species=s000 clade=c00
-        shortLabel GCA_021950905.1 mafNet
-        longLabel GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) mafNet Alignment
+        shortLabel HG002 pat Net
+        longLabel HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Net Alignment
         type bigMaf
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021950905.1.net.bb
         summary bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021950905.1.net.summary.bb
         speciesOrder GCA_021950905.1
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 1
 
         track synNetGCA_021950905.1
         parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
         subGroups view=net species=s000 clade=c00
-        shortLabel GCA_021950905.1 synNet
-        longLabel GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Syntenic Net Alignment
+        shortLabel HG002 pat synNet
+        longLabel HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Syntenic Net Alignment
         type bigMaf
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021950905.1.synNet.bb
         summary bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021950905.1.synNet.summary.bb
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         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 2
 
         track rbestNetGCA_021950905.1
         parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
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-        shortLabel GCA_021950905.1 rbestNet
-        longLabel GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Reciprocal Best Net Alignment
+        shortLabel HG002 pat rbestNet
+        longLabel HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Reciprocal Best Net Alignment
         type bigMaf
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021950905.1.rbestNet.bb
         summary bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021950905.1.rbestNet.summary.bb
         speciesOrder GCA_021950905.1
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 3
 
         track liftOverNetGCA_021950905.1
         parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
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-        shortLabel GCA_021950905.1 liftOverNet
-        longLabel GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Lift Over Net Alignment
+        shortLabel HG002 pat liftOverNet
+        longLabel HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Lift Over Net Alignment
         type bigMaf
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021950905.1.liftOverNet.bb
         summary bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021950905.1.liftOverNet.summary.bb
         speciesOrder GCA_021950905.1
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 4
 
         track netGCA_021951015.1
         parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
         subGroups view=net species=s001 clade=c00
-        shortLabel GCA_021951015.1 mafNet
-        longLabel GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) mafNet Alignment
+        shortLabel HG002 mat Net
+        longLabel HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Net Alignment
         type bigMaf
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021951015.1.net.bb
         summary bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021951015.1.net.summary.bb
         speciesOrder GCA_021951015.1
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 5
 
         track synNetGCA_021951015.1
         parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
         subGroups view=net species=s001 clade=c00
-        shortLabel GCA_021951015.1 synNet
-        longLabel GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Syntenic Net Alignment
+        shortLabel HG002 mat synNet
+        longLabel HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Syntenic Net Alignment
         type bigMaf
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021951015.1.synNet.bb
         summary bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021951015.1.synNet.summary.bb
         speciesOrder GCA_021951015.1
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 6
 
         track rbestNetGCA_021951015.1
         parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
         subGroups view=net species=s001 clade=c00
-        shortLabel GCA_021951015.1 rbestNet
-        longLabel GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Reciprocal Best Net Alignment
+        shortLabel HG002 mat rbestNet
+        longLabel HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Reciprocal Best Net Alignment
         type bigMaf
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021951015.1.rbestNet.bb
         summary bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021951015.1.rbestNet.summary.bb
         speciesOrder GCA_021951015.1
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 7
 
         track liftOverNetGCA_021951015.1
         parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
         subGroups view=net species=s001 clade=c00
-        shortLabel GCA_021951015.1 liftOverNet
-        longLabel GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Lift Over Net Alignment
+        shortLabel HG002 mat liftOverNet
+        longLabel HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Lift Over Net Alignment
         type bigMaf
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021951015.1.liftOverNet.bb
         summary bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021951015.1.liftOverNet.summary.bb
         speciesOrder GCA_021951015.1
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 8
 
         track netHg19
         parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
         subGroups view=net species=s002 clade=c00
-        shortLabel hg19 mafNet
-        longLabel hg19 (Feb. 2009) mafNet Alignment
+        shortLabel hg19 Net
+        longLabel hg19 (Feb. 2009) Net Alignment
         type bigMaf
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.hg19.net.bb
         summary bbi/GCA_009914755.4_T2T-CHM13v2.0.hg19.net.summary.bb
         speciesOrder hg19
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 9
 
         track synNetHg19
         parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
         subGroups view=net species=s002 clade=c00
         shortLabel hg19 synNet
         longLabel hg19 (Feb. 2009) Syntenic Net Alignment
         type bigMaf
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.hg19.synNet.bb
         summary bbi/GCA_009914755.4_T2T-CHM13v2.0.hg19.synNet.summary.bb
         speciesOrder hg19
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 10
 
         track rbestNetHg19
         parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
         subGroups view=net species=s002 clade=c00
         shortLabel hg19 rbestNet
         longLabel hg19 (Feb. 2009) Reciprocal Best Net Alignment
         type bigMaf
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.hg19.rbestNet.bb
         summary bbi/GCA_009914755.4_T2T-CHM13v2.0.hg19.rbestNet.summary.bb
         speciesOrder hg19
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 11
 
         track liftOverNetHg19
         parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
         subGroups view=net species=s002 clade=c00
         shortLabel hg19 liftOverNet
         longLabel hg19 (Feb. 2009) Lift Over Net Alignment
         type bigMaf
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.hg19.liftOverNet.bb
         summary bbi/GCA_009914755.4_T2T-CHM13v2.0.hg19.liftOverNet.summary.bb
         speciesOrder hg19
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 12
 
         track netHg38
         parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
         subGroups view=net species=s003 clade=c00
-        shortLabel hg38 mafNet
-        longLabel hg38 (Dec. 2013) mafNet Alignment
+        shortLabel hg38 Net
+        longLabel hg38 (Dec. 2013) Net Alignment
         type bigMaf
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.hg38.net.bb
         summary bbi/GCA_009914755.4_T2T-CHM13v2.0.hg38.net.summary.bb
         speciesOrder hg38
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 13
 
         track synNetHg38
         parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
         subGroups view=net species=s003 clade=c00
         shortLabel hg38 synNet
         longLabel hg38 (Dec. 2013) Syntenic Net Alignment
         type bigMaf
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.hg38.synNet.bb
         summary bbi/GCA_009914755.4_T2T-CHM13v2.0.hg38.synNet.summary.bb
         speciesOrder hg38
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 14
 
         track rbestNetHg38
         parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
         subGroups view=net species=s003 clade=c00
         shortLabel hg38 rbestNet
         longLabel hg38 (Dec. 2013) Reciprocal Best Net Alignment
         type bigMaf
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.hg38.rbestNet.bb
         summary bbi/GCA_009914755.4_T2T-CHM13v2.0.hg38.rbestNet.summary.bb
         speciesOrder hg38
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 15
 
         track liftOverNetHg38
         parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
         subGroups view=net species=s003 clade=c00
         shortLabel hg38 liftOverNet
         longLabel hg38 (Dec. 2013) Lift Over Net Alignment
         type bigMaf
         bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.hg38.liftOverNet.bb
         summary bbi/GCA_009914755.4_T2T-CHM13v2.0.hg38.liftOverNet.summary.bb
         speciesOrder hg38
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 16
 
 include GCA_009914755.4.userTrackDb.txt