ad6dd2177ad20bea9e32563ee76a1c598bccb6d5
hiram
  Tue Sep 29 23:22:17 2026 -0700
adding hg38 liftOver chain from lastz refs #34360

diff --git src/hg/makeDb/trackDb/human/hs1/humanChainNet.trackDb.ra src/hg/makeDb/trackDb/human/hs1/humanChainNet.trackDb.ra
index 60c2acd837d..d060839988a 100644
--- src/hg/makeDb/trackDb/human/hs1/humanChainNet.trackDb.ra
+++ src/hg/makeDb/trackDb/human/hs1/humanChainNet.trackDb.ra
@@ -1,416 +1,406 @@
 track GCA_009914755.4_T2T-CHM13v2.0ChainNet
 compositeTrack on
 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 full
 group compGeno
 color 0,0,0
 altColor 255,255,0
 type bed 3
 dimensions dimensionX=clade dimensionY=species
 sortOrder species=+ view=+ clade=+
 configurable on
 html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
 priority 1
 
     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 HG002 pat Chain
         longLabel HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Chained Alignments
         type bigChain GCA_021950905.1
         bigDataUrl  /gbdb/hs1/bbi/chainGCA_021950905.1.bb
         linkDataUrl  /gbdb/hs1/bbi/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 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  /gbdb/hs1/bbi/chainSynGCA_021950905.1.bb
         linkDataUrl  /gbdb/hs1/bbi/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 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  /gbdb/hs1/bbi/chainRBestGCA_021950905.1.bb
         linkDataUrl  /gbdb/hs1/bbi/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 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  /gbdb/hs1/bbi/chainLiftOverGCA_021950905.1.bb
         #linkDataUrl  /gbdb/hs1/bbi/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 HG002 mat Chain
         longLabel HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Chained Alignments
         type bigChain GCA_021951015.1
         bigDataUrl  /gbdb/hs1/bbi/chainGCA_021951015.1.bb
         linkDataUrl  /gbdb/hs1/bbi/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 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  /gbdb/hs1/bbi/chainSynGCA_021951015.1.bb
         linkDataUrl  /gbdb/hs1/bbi/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 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  /gbdb/hs1/bbi/chainRBestGCA_021951015.1.bb
         linkDataUrl  /gbdb/hs1/bbi/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 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  /gbdb/hs1/bbi/chainLiftOverGCA_021951015.1.bb
         #linkDataUrl  /gbdb/hs1/bbi/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  /gbdb/hs1/bbi/chainHg19.bb
         linkDataUrl  /gbdb/hs1/bbi/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  /gbdb/hs1/bbi/chainSynHg19.bb
         linkDataUrl  /gbdb/hs1/bbi/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  /gbdb/hs1/bbi/chainRBestHg19.bb
         linkDataUrl  /gbdb/hs1/bbi/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  /gbdb/hs1/bbi/chainLiftOverHg19.bb
         #linkDataUrl  /gbdb/hs1/bbi/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  /gbdb/hs1/bbi/chainHg38.bb
         linkDataUrl  /gbdb/hs1/bbi/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  /gbdb/hs1/bbi/chainSynHg38.bb
         linkDataUrl  /gbdb/hs1/bbi/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  /gbdb/hs1/bbi/chainRBestHg38.bb
         linkDataUrl  /gbdb/hs1/bbi/chainRBestHg38Link.bb
         otherDb hg38
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 15
 
-        #track chainLiftOverHg38
-        #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  /gbdb/hs1/bbi/chainLiftOverHg38.bb
-        #linkDataUrl  /gbdb/hs1/bbi/chainLiftOverHg38Link.bb
-        #otherDb hg38
-        #html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
-        #priority 16
+        include chainLiftOverHg38.ra alpha
 
     track GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
     shortLabel Nets
     view net
     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 HG002 pat Net
         longLabel HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Net Alignment
         type bigMaf
         bigDataUrl  /gbdb/hs1/bbi/GCA_021950905.1.net.bb
         summary /gbdb/hs1/bbi/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 HG002 pat synNet
         longLabel HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Syntenic Net Alignment
         type bigMaf
         bigDataUrl  /gbdb/hs1/bbi/GCA_021950905.1.synNet.bb
         summary /gbdb/hs1/bbi/GCA_021950905.1.synNet.summary.bb
         speciesOrder GCA_021950905.1
         html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         priority 2
 
         track rbestNetGCA_021950905.1
         parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet
         subGroups view=net species=s000 clade=c00
         shortLabel HG002 pat rbestNet
         longLabel HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Reciprocal Best Net Alignment
         type bigMaf
         bigDataUrl  /gbdb/hs1/bbi/GCA_021950905.1.rbestNet.bb
         summary /gbdb/hs1/bbi/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
         #subGroups view=net species=s000 clade=c00
         #shortLabel HG002 pat liftOverNet
         #longLabel HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Lift Over Net Alignment
         #type bigMaf
         #bigDataUrl  /gbdb/hs1/bbi/GCA_021950905.1.liftOverNet.bb
         #summary /gbdb/hs1/bbi/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 HG002 mat Net
         longLabel HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Net Alignment
         type bigMaf
         bigDataUrl  /gbdb/hs1/bbi/GCA_021951015.1.net.bb
         summary /gbdb/hs1/bbi/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 HG002 mat synNet
         longLabel HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Syntenic Net Alignment
         type bigMaf
         bigDataUrl  /gbdb/hs1/bbi/GCA_021951015.1.synNet.bb
         summary /gbdb/hs1/bbi/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 HG002 mat rbestNet
         longLabel HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Reciprocal Best Net Alignment
         type bigMaf
         bigDataUrl  /gbdb/hs1/bbi/GCA_021951015.1.rbestNet.bb
         summary /gbdb/hs1/bbi/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 HG002 mat liftOverNet
         #longLabel HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Lift Over Net Alignment
         #type bigMaf
         #bigDataUrl  /gbdb/hs1/bbi/GCA_021951015.1.liftOverNet.bb
         #summary /gbdb/hs1/bbi/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 Net
         longLabel hg19 (Feb. 2009) Net Alignment
         type bigMaf
         bigDataUrl  /gbdb/hs1/bbi/hg19.net.bb
         summary /gbdb/hs1/bbi/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  /gbdb/hs1/bbi/hg19.synNet.bb
         summary /gbdb/hs1/bbi/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  /gbdb/hs1/bbi/hg19.rbestNet.bb
         summary /gbdb/hs1/bbi/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  /gbdb/hs1/bbi/hg19.liftOverNet.bb
         #summary /gbdb/hs1/bbi/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 Net
         longLabel hg38 (Dec. 2013) Net Alignment
         type bigMaf
         bigDataUrl  /gbdb/hs1/bbi/hg38.net.bb
         summary /gbdb/hs1/bbi/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  /gbdb/hs1/bbi/hg38.synNet.bb
         summary /gbdb/hs1/bbi/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  /gbdb/hs1/bbi/hg38.rbestNet.bb
         summary /gbdb/hs1/bbi/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  /gbdb/hs1/bbi/hg38.liftOverNet.bb
         #summary /gbdb/hs1/bbi/hg38.liftOverNet.summary.bb
         #speciesOrder hg38
         #html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet
         #priority 16