cc5e3c90e84384bb7afc43f35cfa1177e8e5975e hiram Thu Apr 13 13:47:45 2023 -0700 add in the T2T-CHM13v2.0 chains nets refs #30508 diff --git src/hg/makeDb/trackDb/human/chainNetHuman.ra src/hg/makeDb/trackDb/human/chainNetHuman.ra index e0e6534..5d4446f 100644 --- src/hg/makeDb/trackDb/human/chainNetHuman.ra +++ src/hg/makeDb/trackDb/human/chainNetHuman.ra @@ -1,76 +1,116 @@ track humanChainNet compositeTrack on shortLabel Human Chain/Net longLabel Human Genomes, Chain and Net Alignments subGroup1 view Views chain=Chains net=Nets -subGroup2 species Species s000=CHM13 s002=HG01106.mat s003=HG03098.mat s004=HG00735.pat s005=HG01258.mat s006=HG005.mat s007=HG01891.pat s008=HG02055.mat s009=HG00733.mat s010=HG02486.mat s011=HG03516.mat s012=HG02886.mat s013=HG00733.pat s014=HG03516.pat s015=HG02622.pat s016=HG02886.pat s017=HG00741.mat s018=HG00621.mat s019=HG01123.mat s020=HG02257.pat s021=HG00735.mat s022=HG02723.pat s023=HG03453.pat s024=HG01071.pat s025=HG03453.mat s026=HG01952.mat s027=HG00438.pat s028=HG02257.mat s029=HG02559.mat s030=HG01361.pat s031=NA18906.pat s032=HG00438.mat s033=NA18906.mat s034=NA20129.pat s035=HG02080.pat s036=HG002.mat s037=HG01928.mat s038=HG02109.mat s039=HG01978.pat s040=HG01361.mat s041=HG02717.mat s042=HG01123.pat s043=HG02148.mat s044=HG02080.mat s045=HG002.mat.20211005 s046=NA19240.pat s047=HG03492.mat s048=HG00673.mat s049=HG03486.pat s050=HG02630.mat s051=HG02148.pat s052=HG01175.pat s053=HG02630.pat s054=HG01891.mat s055=NA20129.mat s056=HG02818.pat s057=NA21309.pat s058=HG02559.pat s059=HG01358.mat s060=HG00741.pat s061=HG03579.mat s062=NA21309.mat s063=HG02109.pat s064=HG01071.mat s065=HG03540.mat s066=HG02145.mat s067=HG01978.mat s068=HG03486.mat s069=NA19240.mat s070=HG02818.mat s071=HG02723.mat s072=HG02622.mat s073=HG03540.pat s074=HG02572.mat s075=HG01243.mat s076=HG01109.mat s077=HG01175.mat s078=HG00621.pat s079=HG01928.pat s080=HG005.pat s081=HG01106.pat s082=HG01258.pat s083=HG01358.pat s084=HG01109.pat s085=HG02717.pat s086=HG02055.pat s087=HG002.pat s088=HG03492.pat s089=HG00673.pat s090=HG002.pat.20211005 s091=HG01243.pat s092=HG02486.pat s093=HG03579.pat s094=HG02145.pat s095=HG01952.pat s096=HG02572.pat s097=HG03098.pat +subGroup2 species Species s000=CHM13 s002a=T2T-CHM13v2.0 s002b=HG01106.mat s003=HG03098.mat s004=HG00735.pat s005=HG01258.mat s006=HG005.mat s007=HG01891.pat s008=HG02055.mat s009=HG00733.mat s010=HG02486.mat s011=HG03516.mat s012=HG02886.mat s013=HG00733.pat s014=HG03516.pat s015=HG02622.pat s016=HG02886.pat s017=HG00741.mat s018=HG00621.mat s019=HG01123.mat s020=HG02257.pat s021=HG00735.mat s022=HG02723.pat s023=HG03453.pat s024=HG01071.pat s025=HG03453.mat s026=HG01952.mat s027=HG00438.pat s028=HG02257.mat s029=HG02559.mat s030=HG01361.pat s031=NA18906.pat s032=HG00438.mat s033=NA18906.mat s034=NA20129.pat s035=HG02080.pat s036=HG002.mat s037=HG01928.mat s038=HG02109.mat s039=HG01978.pat s040=HG01361.mat s041=HG02717.mat s042=HG01123.pat s043=HG02148.mat s044=HG02080.mat s045=HG002.mat.20211005 s046=NA19240.pat s047=HG03492.mat s048=HG00673.mat s049=HG03486.pat s050=HG02630.mat s051=HG02148.pat s052=HG01175.pat s053=HG02630.pat s054=HG01891.mat s055=NA20129.mat s056=HG02818.pat s057=NA21309.pat s058=HG02559.pat s059=HG01358.mat s060=HG00741.pat s061=HG03579.mat s062=NA21309.mat s063=HG02109.pat s064=HG01071.mat s065=HG03540.mat s066=HG02145.mat s067=HG01978.mat s068=HG03486.mat s069=NA19240.mat s070=HG02818.mat s071=HG02723.mat s072=HG02622.mat s073=HG03540.pat s074=HG02572.mat s075=HG01243.mat s076=HG01109.mat s077=HG01175.mat s078=HG00621.pat s079=HG01928.pat s080=HG005.pat s081=HG01106.pat s082=HG01258.pat s083=HG01358.pat s084=HG01109.pat s085=HG02717.pat s086=HG02055.pat s087=HG002.pat s088=HG03492.pat s089=HG00673.pat s090=HG002.pat.20211005 s091=HG01243.pat s092=HG02486.pat s093=HG03579.pat s094=HG02145.pat s095=HG01952.pat s096=HG02572.pat s097=HG03098.pat subGroup3 mafType Align_type mt0=mafNet mt1=synNet mt2=rbestNet mt3=liftOver dragAndDrop subTracks visibility hide group compGeno noInherit on color 0,0,0 altColor 255,255,0 type bed 3 chainLinearGap loose chainMinScore 5000 dimensions dimensionX=mafType dimensionY=species sortOrder species=+ view=+ mafType=+ configurable on html homoSapiensChainNet track humanChainNetViewchain shortLabel Chains view chain visibility pack subTrack humanChainNet spectrum on + track chainGCA_009914755.4 + parent humanChainNetViewchain + subGroups view=chain species=s002a mafType=mt0 + shortLabel T2T-CHM13v2.0 Chain + longLabel T2T-CHM13v2.0 (May 2021 GCA_009914755.4_T2T-CHM13v2.0) Chained Alignments + type bigChain GCA_009914755.4 + bigDataUrl /gbdb/$D/chainNet/$D.chainGCA_009914755.4.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainGCA_009914755.4Link.bb + otherDb GCA_009914755.4 + + track chainSynGCA_009914755.4 + parent humanChainNetViewchain + subGroups view=chain species=s002a mafType=mt1 + shortLabel T2T-CHM13v2.0 synChain + longLabel T2T-CHM13v2.0 (May 2021 GCA_009914755.4_T2T-CHM13v2.0) Syntenic Chained Alignments + type bigChain GCA_009914755.4 + bigDataUrl /gbdb/$D/chainNet/$D.chainSynGCA_009914755.4.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainSynGCA_009914755.4Link.bb + otherDb GCA_009914755.4 + + track chainRBestGCA_009914755.4 + parent humanChainNetViewchain + subGroups view=chain species=s002a mafType=mt2 + shortLabel T2T-CHM13v2.0 rBestChain + longLabel T2T-CHM13v2.0 (May 2021 GCA_009914755.4_T2T-CHM13v2.0) Reciprocal Best Chained Alignments + type bigChain GCA_009914755.4 + bigDataUrl /gbdb/$D/chainNet/$D.chainRBestGCA_009914755.4.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainRBestGCA_009914755.4Link.bb + otherDb GCA_009914755.4 + + track chainLiftOverGCA_009914755.4 + parent humanChainNetViewchain + subGroups view=chain species=s002a mafType=mt3 + shortLabel T2T-CHM13v2.0 LiftOver Chain + longLabel T2T-CHM13v2.0 (May 2021 GCA_009914755.4_T2T-CHM13v2.0) Lift Over Chained Alignments + type bigChain GCA_009914755.4 + bigDataUrl /gbdb/$D/chainNet/$D.chainLiftOverGCA_009914755.4.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainLiftOverGCA_009914755.4Link.bb + otherDb GCA_009914755.4 + track chainGCA_018471345.1 parent humanChainNetViewchain - subGroups view=chain species=s002 mafType=mt0 + subGroups view=chain species=s002b mafType=mt0 shortLabel HG01106.pri.mat.f1_v2 Chain longLabel HG01106.pri.mat.f1_v2 (May 2021 GCA_018471345.1_HG01106.pri.mat.f1_v2) Chained Alignments type bigChain GCA_018471345.1 bigDataUrl /gbdb/$D/chainNet/$D.chainGCA_018471345.1.bb linkDataUrl /gbdb/$D/chainNet/$D.chainGCA_018471345.1Link.bb otherDb GCA_018471345.1 track chainSynGCA_018471345.1 parent humanChainNetViewchain - subGroups view=chain species=s002 mafType=mt1 + subGroups view=chain species=s002b mafType=mt1 shortLabel HG01106.pri.mat.f1_v2 synChain longLabel HG01106.pri.mat.f1_v2 (May 2021 GCA_018471345.1_HG01106.pri.mat.f1_v2) Syntenic Chained Alignments type bigChain GCA_018471345.1 bigDataUrl /gbdb/$D/chainNet/$D.chainSynGCA_018471345.1.bb linkDataUrl /gbdb/$D/chainNet/$D.chainSynGCA_018471345.1Link.bb otherDb GCA_018471345.1 track chainRBestGCA_018471345.1 parent humanChainNetViewchain - subGroups view=chain species=s002 mafType=mt2 + subGroups view=chain species=s002b mafType=mt2 shortLabel HG01106.pri.mat.f1_v2 rBestChain longLabel HG01106.pri.mat.f1_v2 (May 2021 GCA_018471345.1_HG01106.pri.mat.f1_v2) Reciprocal Best Chained Alignments type bigChain GCA_018471345.1 bigDataUrl /gbdb/$D/chainNet/$D.chainRBestGCA_018471345.1.bb linkDataUrl /gbdb/$D/chainNet/$D.chainRBestGCA_018471345.1Link.bb otherDb GCA_018471345.1 track chainLiftOverGCA_018471345.1 parent humanChainNetViewchain - subGroups view=chain species=s002 mafType=mt3 + subGroups view=chain species=s002b mafType=mt3 shortLabel HG01106.pri.mat.f1_v2 LiftOver Chain longLabel HG01106.pri.mat.f1_v2 (May 2021 GCA_018471345.1_HG01106.pri.mat.f1_v2) Lift Over Chained Alignments type bigChain GCA_018471345.1 bigDataUrl /gbdb/$D/chainNet/$D.chainLiftOverGCA_018471345.1.bb linkDataUrl /gbdb/$D/chainNet/$D.chainLiftOverGCA_018471345.1Link.bb otherDb GCA_018471345.1 track chainGCA_018506165.1 parent humanChainNetViewchain subGroups view=chain species=s003 mafType=mt0 shortLabel HG03098.pri.mat.f1_v2 Chain longLabel HG03098.pri.mat.f1_v2 (May 2021 GCA_018506165.1_HG03098.pri.mat.f1_v2) Chained Alignments type bigChain GCA_018506165.1 bigDataUrl /gbdb/$D/chainNet/$D.chainGCA_018506165.1.bb linkDataUrl /gbdb/$D/chainNet/$D.chainGCA_018506165.1Link.bb @@ -3860,66 +3900,110 @@ parent humanChainNetViewchain subGroups view=chain species=s097 mafType=mt3 shortLabel HG03098.alt.pat.f1_v2 LiftOver Chain longLabel HG03098.alt.pat.f1_v2 (May 2021 GCA_018506155.1_HG03098.alt.pat.f1_v2) Lift Over Chained Alignments type bigChain GCA_018506155.1 bigDataUrl /gbdb/$D/chainNet/$D.chainLiftOverGCA_018506155.1.bb linkDataUrl /gbdb/$D/chainNet/$D.chainLiftOverGCA_018506155.1Link.bb otherDb GCA_018506155.1 track humanMafNetViewnet shortLabel Nets view net visibility dense subTrack humanChainNet + track netGCA_009914755.4 + parent humanMafNetViewnet + subGroups view=net species=s002a mafType=mt0 + shortLabel T2T-CHM13v2.0 mafNet + longLabel T2T-CHM13v2.0 (May 2021 GCA_009914755.4_T2T-CHM13v2.0) mafNet Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_009914755.4.net.bb + summary /gbdb/$D/chainNet/$D.GCA_009914755.4.net.summary.bb + speciesOrder GCA_009914755.4 + speciesLabels GCA_009914755.4="T2T-CHM13v2.0" + + track synNetGCA_009914755.4 + parent humanMafNetViewnet + subGroups view=net species=s002a mafType=mt1 + shortLabel T2T-CHM13v2.0 synNet + longLabel T2T-CHM13v2.0 (May 2021 GCA_009914755.4_T2T-CHM13v2.0) Syntenic Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_009914755.4.synNet.bb + summary /gbdb/$D/chainNet/$D.GCA_009914755.4.synNet.summary.bb + speciesOrder GCA_009914755.4 + speciesLabels GCA_009914755.4="T2T-CHM13v2.0" + + track rbestNetGCA_009914755.4 + parent humanMafNetViewnet + subGroups view=net species=s002a mafType=mt2 + shortLabel T2T-CHM13v2.0 rBestNet + longLabel T2T-CHM13v2.0 (May 2021 GCA_009914755.4_T2T-CHM13v2.0) Reciprocal Best Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_009914755.4.rbestNet.bb + summary /gbdb/$D/chainNet/$D.GCA_009914755.4.rbestNet.summary.bb + speciesOrder GCA_009914755.4 + speciesLabels GCA_009914755.4="T2T-CHM13v2.0" + + track liftOverNetGCA_009914755.4 + parent humanMafNetViewnet + subGroups view=net species=s002a mafType=mt3 + shortLabel T2T-CHM13v2.0 liftOverNet + longLabel T2T-CHM13v2.0 (May 2021 GCA_009914755.4_T2T-CHM13v2.0) Lift Over Best Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_009914755.4.liftOverNet.bb + summary /gbdb/$D/chainNet/$D.GCA_009914755.4.liftOverNet.summary.bb + speciesOrder GCA_009914755.4 + speciesLabels GCA_009914755.4="T2T-CHM13v2.0" + track netGCA_018471345.1 parent humanMafNetViewnet - subGroups view=net species=s002 mafType=mt0 + subGroups view=net species=s002b mafType=mt0 shortLabel HG01106.pri.mat.f1_v2 mafNet longLabel HG01106.pri.mat.f1_v2 (May 2021 GCA_018471345.1_HG01106.pri.mat.f1_v2) mafNet Alignment type bigMaf bigDataUrl /gbdb/$D/chainNet/$D.GCA_018471345.1.net.bb summary /gbdb/$D/chainNet/$D.GCA_018471345.1.net.summary.bb speciesOrder GCA_018471345.1 speciesLabels GCA_018471345.1="HG01106.pri.mat.f1_v2" track synNetGCA_018471345.1 parent humanMafNetViewnet - subGroups view=net species=s002 mafType=mt1 + subGroups view=net species=s002b mafType=mt1 shortLabel HG01106.pri.mat.f1_v2 synNet longLabel HG01106.pri.mat.f1_v2 (May 2021 GCA_018471345.1_HG01106.pri.mat.f1_v2) Syntenic Net Alignment type bigMaf bigDataUrl /gbdb/$D/chainNet/$D.GCA_018471345.1.synNet.bb summary /gbdb/$D/chainNet/$D.GCA_018471345.1.synNet.summary.bb speciesOrder GCA_018471345.1 speciesLabels GCA_018471345.1="HG01106.pri.mat.f1_v2" track rbestNetGCA_018471345.1 parent humanMafNetViewnet - subGroups view=net species=s002 mafType=mt2 + subGroups view=net species=s002b mafType=mt2 shortLabel HG01106.pri.mat.f1_v2 rBestNet longLabel HG01106.pri.mat.f1_v2 (May 2021 GCA_018471345.1_HG01106.pri.mat.f1_v2) Reciprocal Best Net Alignment type bigMaf bigDataUrl /gbdb/$D/chainNet/$D.GCA_018471345.1.rbestNet.bb summary /gbdb/$D/chainNet/$D.GCA_018471345.1.rbestNet.summary.bb speciesOrder GCA_018471345.1 speciesLabels GCA_018471345.1="HG01106.pri.mat.f1_v2" track liftOverNetGCA_018471345.1 parent humanMafNetViewnet - subGroups view=net species=s002 mafType=mt3 + subGroups view=net species=s002b mafType=mt3 shortLabel HG01106.pri.mat.f1_v2 liftOverNet longLabel HG01106.pri.mat.f1_v2 (May 2021 GCA_018471345.1_HG01106.pri.mat.f1_v2) Lift Over Best Net Alignment type bigMaf bigDataUrl /gbdb/$D/chainNet/$D.GCA_018471345.1.liftOverNet.bb summary /gbdb/$D/chainNet/$D.GCA_018471345.1.liftOverNet.summary.bb speciesOrder GCA_018471345.1 speciesLabels GCA_018471345.1="HG01106.pri.mat.f1_v2" track netGCA_018506165.1 parent humanMafNetViewnet subGroups view=net species=s003 mafType=mt0 shortLabel HG03098.pri.mat.f1_v2 mafNet longLabel HG03098.pri.mat.f1_v2 (May 2021 GCA_018506165.1_HG03098.pri.mat.f1_v2) mafNet Alignment type bigMaf bigDataUrl /gbdb/$D/chainNet/$D.GCA_018506165.1.net.bb