478769000cef7d4756c3cdc13c0d61d698f08a2b hiram Thu Aug 24 19:39:05 2023 -0700 adding chainNet definitions for GCA_018873775.2_hg01243.v3.0 refs #31844 diff --git src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra index 4833f44..de85eb4 100644 --- src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra +++ src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra @@ -1,1000 +1,1098 @@ ############################################################################## # hs1/ GCA_009914755.4_CHM13_T2T_v2.0 - human - Homo sapiens - taxId: 9606 - primate ############################################################################## track chainNetHs1 compositeTrack on shortLabel hs1/CHM13 T2T Chain/Net longLabel hs1/CHM13 T2T (Jan. 2022 hs1/GCA_009914755.4_CHM13_T2T_v2.0), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno noInherit on priority 100.1 color 0,0,0 altColor 100,50,0 type bed 3 sortOrder view=+ matrix 16 90,-330,-236,-356,-330,100,-318,-236,-236,-318,100,-330,-356,-236,-330,90 chainMinScore 5000 chainLinearGap medium matrixHeader A, C, G, T otherDb hs1 html chainNet track chainNetHs1Viewchain shortLabel Chain view chain visibility pack parent chainNetHs1 spectrum on track chainHs1 parent chainNetHs1Viewchain subGroups view=chain shortLabel hs1/CHM13 T2T Chain longLabel hs1/CHM13 T2T (Jan. 2022 hs1/GCA_009914755.4_CHM13_T2T_v2.0) Chained Alignments type bigChain hs1 bigDataUrl /gbdb/$D/chainNet/$D.chainHs1.bb linkDataUrl /gbdb/$D/chainNet/$D.chainHs1Link.bb track chainSynHs1 parent chainNetHs1Viewchain subGroups view=chain shortLabel hs1/CHM13 T2T Chain longLabel hs1/CHM13 T2T (Jan. 2022 hs1/GCA_009914755.4_CHM13_T2T_v2.0) Syntenic Chained Alignments type bigChain hs1 bigDataUrl /gbdb/$D/chainNet/$D.chainSynHs1.bb linkDataUrl /gbdb/$D/chainNet/$D.chainSynHs1Link.bb track chainRBestHs1 parent chainNetHs1Viewchain subGroups view=chain shortLabel hs1/CHM13 T2T Chain longLabel hs1/CHM13 T2T (Jan. 2022 hs1/GCA_009914755.4_CHM13_T2T_v2.0) Reciprocal Best Chained Alignments type bigChain hs1 bigDataUrl /gbdb/$D/chainNet/$D.chainRBestHs1.bb linkDataUrl /gbdb/$D/chainNet/$D.chainRBestHs1Link.bb track mafNetHs1Viewnet shortLabel Net view net visibility full parent chainNetHs1 track netHs1 parent mafNetHs1Viewnet subGroups view=net shortLabel hs1/CHM13 T2T mafNet longLabel hs1/CHM13 T2T (Jan. 2022 hs1/GCA_009914755.4_CHM13_T2T_v2.0) mafNet Alignment type bigMaf bigDataUrl /gbdb/$D/chainNet/$D.hs1.net.bb summary /gbdb/$D/chainNet/$D.hs1.net.summary.bb speciesOrder hs1 speciesLabels hs1="CHM13 T2T" track synNetHs1 parent mafNetHs1Viewnet subGroups view=net shortLabel hs1/CHM13 T2T mafNet longLabel hs1/CHM13 T2T (Jan. 2022 hs1/GCA_009914755.4_CHM13_T2T_v2.0) Syntenic Net Alignment type bigMaf bigDataUrl /gbdb/$D/chainNet/$D.hs1.synNet.bb summary /gbdb/$D/chainNet/$D.hs1.synNet.summary.bb speciesOrder hs1 speciesLabels hs1="CHM13 T2T" track rbestNetHs1 parent mafNetHs1Viewnet subGroups view=net shortLabel hs1/CHM13 T2T mafNet longLabel hs1/CHM13 T2T (Jan. 2022 hs1/GCA_009914755.4_CHM13_T2T_v2.0) Reciprocal Best Net Alignment type bigMaf bigDataUrl /gbdb/$D/chainNet/$D.hs1.rbestNet.bb summary /gbdb/$D/chainNet/$D.hs1.rbestNet.summary.bb speciesOrder hs1 speciesLabels hs1="CHM13 T2T" ############################################################################## # GCA_009914755.4_CHM13_T2T_v2.0 - human - Homo sapiens - taxId: 9606 - primate ############################################################################## track chainNetGCA_009914755.4 compositeTrack on shortLabel CHM13 T2T Chain/Net longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno noInherit on priority 100.1 color 0,0,0 altColor 100,50,0 type bed 3 sortOrder view=+ matrix 16 90,-330,-236,-356,-330,100,-318,-236,-236,-318,100,-330,-356,-236,-330,90 chainMinScore 5000 chainLinearGap medium matrixHeader A, C, G, T otherDb GCA_009914755.4 html chainNet track chainNetGCA_009914755.4Viewchain shortLabel Chain view chain visibility pack parent chainNetGCA_009914755.4 spectrum on track chainGCA_009914755.4 parent chainNetGCA_009914755.4Viewchain subGroups view=chain shortLabel CHM13 T2T Chain longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Chained Alignments type bigChain GCA_009914755.4 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCA_009914755.4.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCA_009914755.4Link.bb track chainSynGCA_009914755.4 parent chainNetGCA_009914755.4Viewchain subGroups view=chain shortLabel CHM13 T2T Chain longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Syntenic Chained Alignments type bigChain GCA_009914755.4 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCA_009914755.4.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCA_009914755.4Link.bb track chainRBestGCA_009914755.4 parent chainNetGCA_009914755.4Viewchain subGroups view=chain shortLabel CHM13 T2T Chain longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Reciprocal Best Chained Alignments type bigChain GCA_009914755.4 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCA_009914755.4.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCA_009914755.4Link.bb track mafNetGCA_009914755.4Viewnet shortLabel Net view net visibility full parent chainNetGCA_009914755.4 track netGCA_009914755.4 parent mafNetGCA_009914755.4Viewnet subGroups view=net shortLabel CHM13 T2T mafNet longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) mafNet Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.net.bb summary /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.net.summary.bb speciesOrder GCA_009914755.4 speciesLabels GCA_009914755.4="CHM13 T2T" track synNetGCA_009914755.4 parent mafNetGCA_009914755.4Viewnet subGroups view=net shortLabel CHM13 T2T mafNet longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Syntenic Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.synNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.synNet.summary.bb speciesOrder GCA_009914755.4 speciesLabels GCA_009914755.4="CHM13 T2T" track rbestNetGCA_009914755.4 parent mafNetGCA_009914755.4Viewnet subGroups view=net shortLabel CHM13 T2T mafNet longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Reciprocal Best Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.rbestNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.rbestNet.summary.bb speciesOrder GCA_009914755.4 speciesLabels GCA_009914755.4="CHM13 T2T" ############################################################################## # GCA_901343595v1_MONAX5 - woodchuck - Marmota monax - mammal ############################################################################## track chainNetGCA_901343595v1 compositeTrack on shortLabel $o_Organism Chain/Net longLabel $o_Organism ($o_date), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno noInherit on priority 200.3 color 0,0,0 altColor 255,255,0 type bed 3 sortOrder view=+ matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 matrixHeader A, C, G, T otherDb GCA_901343595v1 chainMinScore 3000 chainLinearGap medium spectrum on html chainNet track chainNetGCA_901343595v1Viewchain shortLabel Chain view chain visibility pack parent chainNetGCA_901343595v1 spectrum on track chainGCA_901343595v1_MONAX5 parent chainNetGCA_901343595v1Viewchain subGroups view=chain shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain GCA_901343595v1 track chainNetGCA_901343595v1Viewnet shortLabel Net view net visibility dense parent chainNetGCA_901343595v1 track netGCA_901343595v1_MONAX5 parent chainNetGCA_901343595v1Viewnet subGroups view=net shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign GCA_901343595v1 chainGCA_901343595v1_MONAX5 ############################################################################## # GCF_003668045.3 - Chinese hamster - Cricetulus griseus - taxId: 10029 - mammal ############################################################################## track chainNetGCF_003668045.3 compositeTrack on shortLabel Chinese hamster Chain/Net longLabel Chinese hamster (Jun. 2020 GCF_003668045.3_CriGri-PICRH-1.0), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno noInherit on priority 100.1 color 0,0,0 altColor 100,50,0 type bed 3 sortOrder view=+ matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 chainLinearGap medium chainMinScore 3000 matrixHeader A, C, G, T otherDb GCF_003668045.3 html chainNet track chainNetGCF_003668045.3Viewchain shortLabel Chain view chain visibility pack parent chainNetGCF_003668045.3 spectrum on track chainGCF_003668045.3 parent chainNetGCF_003668045.3Viewchain subGroups view=chain shortLabel Chinese hamster Chain longLabel Chinese hamster (Jun. 2020 GCF_003668045.3_CriGri-PICRH-1.0) Chained Alignments type bigChain GCF_003668045.3 bigDataUrl /gbdb/$D/bbi/chainNet/chainGCF_003668045.3.bb linkDataUrl /gbdb/$D/bbi/chainNet/chainGCF_003668045.3Link.bb track mafNetGCF_003668045.3Viewnet shortLabel Net view net visibility full parent chainNetGCF_003668045.3 track netGCF_003668045.3 parent mafNetGCF_003668045.3Viewnet subGroups view=net shortLabel Chinese hamster mafNet longLabel Chinese hamster (Jun. 2020 GCF_003668045.3_CriGri-PICRH-1.0) mafNet Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_003668045.3.net.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_003668045.3.net.summary.bb speciesOrder GCF_003668045.3 speciesLabels GCF_003668045.3="Chinese hamster" ############################################################################## # GCF_009829145.1 - lance-tailed manakin - Chiroxiphia lanceolata - taxId: 296741 - birds ############################################################################## track chainNetGCF_009829145.1 compositeTrack on shortLabel lance-tailed manakin Chain/Net longLabel lance-tailed manakin (Jan. 2020 GCF_009829145.1_bChiLan1.pri), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno noInherit on priority 100.1 color 0,0,0 altColor 100,50,0 type bed 3 sortOrder view=+ matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 chainMinScore 3000 chainLinearGap medium matrixHeader A, C, G, T otherDb GCF_009829145.1 html chainNet track chainNetGCF_009829145.1Viewchain shortLabel Chain view chain visibility pack parent chainNetGCF_009829145.1 spectrum on track chainGCF_009829145.1 parent chainNetGCF_009829145.1Viewchain subGroups view=chain shortLabel lance-tailed manakin Chain longLabel lance-tailed manakin (Jan. 2020 GCF_009829145.1_bChiLan1.pri) Chained Alignments type bigChain GCF_009829145.1 bigDataUrl /gbdb/$D/bbi/chainNet/chainGCF_009829145.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/chainGCF_009829145.1Link.bb track mafNetGCF_009829145.1Viewnet shortLabel Net view net visibility full parent chainNetGCF_009829145.1 track netGCF_009829145.1 parent mafNetGCF_009829145.1Viewnet subGroups view=net shortLabel lance-tailed manakin mafNet longLabel lance-tailed manakin (Jan. 2020 GCF_009829145.1_bChiLan1.pri) mafNet Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_009829145.1.net.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_009829145.1.net.summary.bb speciesOrder GCF_009829145.1 speciesLabels GCF_009829145.1="lance-tailed manakin" ############################################################################## # GCF_002742125.1 - Rambouillet sheep - Ovis aries - taxId: 9940 - mammal ############################################################################## track chainNetGCF_002742125.1 compositeTrack on shortLabel Rambouillet sheep Chain/Net longLabel Rambouillet sheep (Nov. 2017 GCF_002742125.1_Oar_rambouillet_v1.0), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno noInherit on priority 100.1 color 0,0,0 altColor 100,50,0 type bed 3 sortOrder view=+ matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 chainMinScore 3000 chainLinearGap medium matrixHeader A, C, G, T otherDb GCF_002742125.1 html chainNet track chainNetGCF_002742125.1Viewchain shortLabel Chain view chain visibility pack parent chainNetGCF_002742125.1 spectrum on track chainGCF_002742125.1 parent chainNetGCF_002742125.1Viewchain subGroups view=chain shortLabel Rambouillet sheep Chain longLabel Rambouillet sheep (Nov. 2017 GCF_002742125.1_Oar_rambouillet_v1.0) Chained Alignments type bigChain GCF_002742125.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_002742125.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_002742125.1Link.bb track chainSynGCF_002742125.1 parent chainNetGCF_002742125.1Viewchain subGroups view=chain shortLabel Rambouillet sheep Chain longLabel Rambouillet sheep (Nov. 2017 GCF_002742125.1_Oar_rambouillet_v1.0) Syntenic Chained Alignments type bigChain GCF_002742125.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_002742125.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_002742125.1Link.bb track chainRBestGCF_002742125.1 parent chainNetGCF_002742125.1Viewchain subGroups view=chain shortLabel Rambouillet sheep Chain longLabel Rambouillet sheep (Nov. 2017 GCF_002742125.1_Oar_rambouillet_v1.0) Reciprocal Best Chained Alignments type bigChain GCF_002742125.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_002742125.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_002742125.1Link.bb track mafNetGCF_002742125.1Viewnet shortLabel Net view net visibility full parent chainNetGCF_002742125.1 track netGCF_002742125.1 parent mafNetGCF_002742125.1Viewnet subGroups view=net shortLabel Rambouillet sheep mafNet longLabel Rambouillet sheep (Nov. 2017 GCF_002742125.1_Oar_rambouillet_v1.0) mafNet Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_002742125.1.net.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_002742125.1.net.summary.bb speciesOrder GCF_002742125.1 speciesLabels GCF_002742125.1="Rambouillet sheep" track synNetGCF_002742125.1 parent mafNetGCF_002742125.1Viewnet subGroups view=net shortLabel Rambouillet sheep mafNet longLabel Rambouillet sheep (Nov. 2017 GCF_002742125.1_Oar_rambouillet_v1.0) Syntenic Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_002742125.1.synNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_002742125.1.synNet.summary.bb speciesOrder GCF_002742125.1 speciesLabels GCF_002742125.1="Rambouillet sheep" track rbestNetGCF_002742125.1 parent mafNetGCF_002742125.1Viewnet subGroups view=net shortLabel Rambouillet sheep mafNet longLabel Rambouillet sheep (Nov. 2017 GCF_002742125.1_Oar_rambouillet_v1.0) Reciprocal Best Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_002742125.1.rbestNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_002742125.1.rbestNet.summary.bb speciesOrder GCF_002742125.1 speciesLabels GCF_002742125.1="Rambouillet sheep" ############################################################################## # GCA_018400075.1 - Zebrafish T5D - Danio rerio - taxId: 7955 - fish ############################################################################## track chainNetGCA_018400075.1 compositeTrack on shortLabel Zebrafish T5D Chain/Net longLabel Zebrafish T5D (May 2021 GCA_018400075.1_ASM1840007v1), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno noInherit on priority 100.1 color 0,0,0 altColor 100,50,0 type bed 3 sortOrder view=+ matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 chainMinScore 5000 chainLinearGap loose matrixHeader A, C, G, T otherDb GCA_018400075.1 html chainNet track chainNetGCA_018400075.1Viewchain shortLabel Chain view chain visibility pack parent chainNetGCA_018400075.1 spectrum on track chainGCA_018400075.1 parent chainNetGCA_018400075.1Viewchain subGroups view=chain shortLabel Zebrafish T5D Chain longLabel Zebrafish T5D (May 2021 GCA_018400075.1_ASM1840007v1) Chained Alignments type bigChain GCA_018400075.1 bigDataUrl /gbdb/$D/bbi/chainNet/chainGCA_018400075.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/chainGCA_018400075.1Link.bb track mafNetGCA_018400075.1Viewnet shortLabel Net view net visibility full parent chainNetGCA_018400075.1 track netGCA_018400075.1 parent mafNetGCA_018400075.1Viewnet subGroups view=net shortLabel Zebrafish T5D mafNet longLabel Zebrafish T5D (May 2021 GCA_018400075.1_ASM1840007v1) mafNet Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_018400075.1.net.bb summary /gbdb/$D/bbi/chainNet/$D.GCA_018400075.1.net.summary.bb speciesOrder GCA_018400075.1 speciesLabels GCA_018400075.1="Zebrafish T5D" ############################################################################## # GCF_016699485.2 - chicken (matMap) - Gallus gallus - taxId: 9031 - birds ############################################################################## track chainNetGCF_016699485.2 compositeTrack on shortLabel Chicken Chain/Net longLabel Chicken (Jan. 2021 (GRCg7b/GCF_016699485.2)), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno noInherit on priority 100.1 color 0,0,0 altColor 100,50,0 type bed 3 sortOrder view=+ matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 chainMinScore 5000 chainLinearGap loose matrixHeader A, C, G, T otherDb GCF_016699485.2 html chainNet track chainNetGCF_016699485.2Viewchain shortLabel Chain view chain visibility pack parent chainNetGCF_016699485.2 spectrum on track chainGCF_016699485.2 parent chainNetGCF_016699485.2Viewchain subGroups view=chain shortLabel Chicken Chain longLabel Chicken (Jan. 2021 (GRCg7b/GCF_016699485.2)) Chained Alignments type bigChain GCF_016699485.2 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_016699485.2.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_016699485.2Link.bb track chainSynGCF_016699485.2 parent chainNetGCF_016699485.2Viewchain subGroups view=chain shortLabel Chicken synChain longLabel Chicken (Jan. 2021 (GRCg7b/GCF_016699485.2)) Syntenic Chained Alignments type bigChain GCF_016699485.2 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_016699485.2.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_016699485.2Link.bb track chainRBestGCF_016699485.2 parent chainNetGCF_016699485.2Viewchain subGroups view=chain shortLabel Chicken rbChain longLabel Chicken (Jan. 2021 (GRCg7b/GCF_016699485.2)) Reciprocal Best Chained Alignments type bigChain GCF_016699485.2 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_016699485.2.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_016699485.2Link.bb track mafNetGCF_016699485.2Viewnet shortLabel Net view net visibility full parent chainNetGCF_016699485.2 track netGCF_016699485.2 parent mafNetGCF_016699485.2Viewnet subGroups view=net shortLabel Chicken net longLabel Chicken (Jan. 2021 (GRCg7b/GCF_016699485.2)) Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_016699485.2.net.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_016699485.2.net.summary.bb speciesOrder GCF_016699485.2 speciesLabels GCF_016699485.2="Chicken/GRCg7b" track synNetGCF_016699485.2 parent mafNetGCF_016699485.2Viewnet subGroups view=net shortLabel Chicken synNet longLabel Chicken (Jan. 2021 (GRCg7b/GCF_016699485.2)) Syntenic Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_016699485.2.synNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_016699485.2.synNet.summary.bb speciesOrder GCF_016699485.2 speciesLabels GCF_016699485.2="Chicken/GRCg7b" track rbestNetGCF_016699485.2 parent mafNetGCF_016699485.2Viewnet subGroups view=net shortLabel Chicken rbestNet longLabel Chicken (Jan. 2021 (GRCg7b/GCF_016699485.2)) Reciprocal Best Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_016699485.2.rbestNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_016699485.2.rbestNet.summary.bb speciesOrder GCF_016699485.2 speciesLabels GCF_016699485.2="Chicken/GRCg7b" ############################################################################## # GCF_000349665.1 - golden hamster - Gallus gallus - taxId: 9031 - birds ############################################################################## track chainNetGCF_000349665.1 compositeTrack on shortLabel Golden hamster Chain/Net longLabel Golden hamster (Mar. 2013 (MesAur1.0/GCF_000349665.1), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno noInherit on priority 100.1 color 0,0,0 altColor 100,50,0 type bed 3 sortOrder view=+ matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 chainMinScore 5000 chainLinearGap loose matrixHeader A, C, G, T otherDb GCF_000349665.1 html chainNet track chainNetGCF_000349665.1iewchain shortLabel Chain view chain visibility pack parent chainNetGCF_000349665.1 spectrum on track chainGCF_000349665.1 parent chainNetGCF_000349665.1iewchain subGroups view=chain shortLabel Golden hamster Chain longLabel Golden hamster (Mar. 2013 (MesAur1.0/GCF_000349665.1) Chained Alignments type bigChain GCF_000349665.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_000349665.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_000349665.1Link.bb track chainSynGCF_000349665.1 parent chainNetGCF_000349665.1iewchain subGroups view=chain shortLabel Golden hamster synChain longLabel Golden hamster (Mar. 2013 (MesAur1.0/GCF_000349665.1) Syntenic Chained Alignments type bigChain GCF_000349665.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_000349665.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_000349665.1Link.bb track chainRBestGCF_000349665.1 parent chainNetGCF_000349665.1iewchain subGroups view=chain shortLabel Golden hamster rbChain longLabel Golden hamster (Mar. 2013 (MesAur1.0/GCF_000349665.1) Reciprocal Best Chained Alignments type bigChain GCF_000349665.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_000349665.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_000349665.1Link.bb track mafNetGCF_000349665.1iewnet shortLabel Net view net visibility full parent chainNetGCF_000349665.1 track netGCF_000349665.1 parent mafNetGCF_000349665.1iewnet subGroups view=net shortLabel Golden hamster net longLabel Golden hamster (Mar. 2013 (MesAur1.0/GCF_000349665.1) Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_000349665.1.net.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_000349665.1.net.summary.bb speciesOrder GCF_000349665.1 speciesLabels GCF_000349665.1="Golden hamster" track synNetGCF_000349665.1 parent mafNetGCF_000349665.1iewnet subGroups view=net shortLabel Golden hamster synNet longLabel Golden hamster (Mar. 2013 (MesAur1.0/GCF_000349665.1) Syntenic Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_000349665.1.synNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_000349665.1.synNet.summary.bb speciesOrder GCF_000349665.1 speciesLabels GCF_000349665.1="Golden hamster" track rbestNetGCF_000349665.1 parent mafNetGCF_000349665.1iewnet subGroups view=net shortLabel Golden hamster rbestNet longLabel Golden hamster (Mar. 2013 (MesAur1.0/GCF_000349665.1) Reciprocal Best Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_000349665.1.rbestNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_000349665.1.rbestNet.summary.bb speciesOrder GCF_000349665.1 speciesLabels GCF_000349665.1="Golden hamster" ############################################################################## # GCF_024166365.1 - Asiatic elephant - Elephas maximus indicus - taxId: 99487 - mammals ############################################################################## track chainNetGCF_024166365.1 compositeTrack on shortLabel Asiatic elephant Chain/Net longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1 primary haplotype), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno noInherit on priority 100.1 color 0,0,0 altColor 100,50,0 type bed 3 sortOrder view=+ matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 chainMinScore 3000 chainLinearGap medium matrixHeader A, C, G, T otherDb GCF_024166365.1 html chainNet track chainNetGCF_024166365.1Viewchain shortLabel Chain view chain visibility pack parent chainNetGCF_024166365.1 spectrum on track chainGCF_024166365.1 parent chainNetGCF_024166365.1Viewchain subGroups view=chain shortLabel Asiatic elephant Chain longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1 primary haplotype) Chained Alignments type bigChain GCF_024166365.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_024166365.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_024166365.1Link.bb track chainSynGCF_024166365.1 parent chainNetGCF_024166365.1Viewchain subGroups view=chain shortLabel Asiatic elephant synChain longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1 primary haplotype) Syntenic Chained Alignments type bigChain GCF_024166365.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_024166365.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_024166365.1Link.bb track chainRBestGCF_024166365.1 parent chainNetGCF_024166365.1Viewchain subGroups view=chain shortLabel Asiatic elephant rBestChain longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1 primary haplotype) Reciprocal Best Chained Alignments type bigChain GCF_024166365.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_024166365.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_024166365.1Link.bb track mafNetGCF_024166365.1Viewnet shortLabel Net view net visibility full parent chainNetGCF_024166365.1 track netGCF_024166365.1 parent mafNetGCF_024166365.1Viewnet subGroups view=net shortLabel Asiatic elephant mafNet longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1 primary haplotype) mafNet Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_024166365.1.net.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_024166365.1.net.summary.bb speciesOrder GCF_024166365.1 speciesLabels GCF_024166365.1="Asiatic elephant" track synNetGCF_024166365.1 parent mafNetGCF_024166365.1Viewnet subGroups view=net shortLabel Asiatic elephant synNet longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1 primary haplotype) Syntenic Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_024166365.1.synNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_024166365.1.synNet.summary.bb speciesOrder GCF_024166365.1 speciesLabels GCF_024166365.1="Asiatic elephant" track rbestNetGCF_024166365.1 parent mafNetGCF_024166365.1Viewnet subGroups view=net shortLabel Asiatic elephant rBestNet longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1 primary haplotype) Reciprocal Best Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_024166365.1.rbestNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_024166365.1.rbestNet.summary.bb speciesOrder GCF_024166365.1 speciesLabels GCF_024166365.1="Asiatic elephant" ############################################################################## # GCF_018350175.1 - domestic cat - Felis catus - taxId: 9685 - mammals ############################################################################## track chainNetGCF_018350175.1 compositeTrack on shortLabel domestic cat Chain/Net longLabel domestic cat (May 2021 GCF_018350175.1_F.catus_Fca126_mat1.0), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno noInherit on priority 100.1 color 0,0,0 altColor 100,50,0 type bed 3 sortOrder view=+ matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 chainMinScore 3000 chainLinearGap medium matrixHeader A, C, G, T otherDb GCF_018350175.1 html chainNet track chainNetGCF_018350175.1Viewchain shortLabel Chain view chain visibility pack parent chainNetGCF_018350175.1 spectrum on track chainGCF_018350175.1 parent chainNetGCF_018350175.1Viewchain subGroups view=chain shortLabel domestic cat Chain longLabel domestic cat (May 2021 GCF_018350175.1_F.catus_Fca126_mat1.0) Chained Alignments type bigChain GCF_018350175.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_018350175.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_018350175.1Link.bb track chainSynGCF_018350175.1 parent chainNetGCF_018350175.1Viewchain subGroups view=chain shortLabel domestic cat synChain longLabel domestic cat (May 2021 GCF_018350175.1_F.catus_Fca126_mat1.0) Syntenic Chained Alignments type bigChain GCF_018350175.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_018350175.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_018350175.1Link.bb track chainRBestGCF_018350175.1 parent chainNetGCF_018350175.1Viewchain subGroups view=chain shortLabel domestic cat rBestChain longLabel domestic cat (May 2021 GCF_018350175.1_F.catus_Fca126_mat1.0) Reciprocal Best Chained Alignments type bigChain GCF_018350175.1 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_018350175.1.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_018350175.1Link.bb track mafNetGCF_018350175.1Viewnet shortLabel Net view net visibility full parent chainNetGCF_018350175.1 track netGCF_018350175.1 parent mafNetGCF_018350175.1Viewnet subGroups view=net shortLabel domestic cat mafNet longLabel domestic cat (May 2021 GCF_018350175.1_F.catus_Fca126_mat1.0) mafNet Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_018350175.1.net.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_018350175.1.net.summary.bb speciesOrder GCF_018350175.1 speciesLabels GCF_018350175.1="domestic cat" track synNetGCF_018350175.1 parent mafNetGCF_018350175.1Viewnet subGroups view=net shortLabel domestic cat synNet longLabel domestic cat (May 2021 GCF_018350175.1_F.catus_Fca126_mat1.0) Syntenic Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_018350175.1.synNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_018350175.1.synNet.summary.bb speciesOrder GCF_018350175.1 speciesLabels GCF_018350175.1="domestic cat" track rbestNetGCF_018350175.1 parent mafNetGCF_018350175.1Viewnet subGroups view=net shortLabel domestic cat rBestNet longLabel domestic cat (May 2021 GCF_018350175.1_F.catus_Fca126_mat1.0) Reciprocal Best Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_018350175.1.rbestNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_018350175.1.rbestNet.summary.bb speciesOrder GCF_018350175.1 speciesLabels GCF_018350175.1="domestic cat" ############################################################################## # GCF_004115215.2 - platypus - Ornithorhynchus anatinus - taxId: 9258 - mammals ############################################################################## track chainNetGCF_004115215.2 compositeTrack on shortLabel platypus Chain/Net longLabel platypus (Nov. 2020 GCF_004115215.2_mOrnAna1.pri.v4), Chain and Net Alignments subGroup1 view Views chain=Chain net=Net dragAndDrop subTracks visibility hide group compGeno noInherit on priority 540.3 color 0,0,0 altColor 100,50,0 type bed 3 sortOrder view=+ matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91 chainMinScore 3000 chainLinearGap medium matrixHeader A, C, G, T otherDb GCF_004115215.2 html chainNet track chainNetGCF_004115215.2Viewchain shortLabel Chain view chain visibility pack parent chainNetGCF_004115215.2 spectrum on track chainGCF_004115215.2 parent chainNetGCF_004115215.2Viewchain subGroups view=chain shortLabel platypus Chain longLabel platypus (Nov. 2020 GCF_004115215.2_mOrnAna1.pri.v4) Chained Alignments type bigChain GCF_004115215.2 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_004115215.2.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_004115215.2Link.bb track chainSynGCF_004115215.2 parent chainNetGCF_004115215.2Viewchain subGroups view=chain shortLabel platypus synChain longLabel platypus (Nov. 2020 GCF_004115215.2_mOrnAna1.pri.v4) Syntenic Chained Alignments type bigChain GCF_004115215.2 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_004115215.2.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_004115215.2Link.bb track chainRBestGCF_004115215.2 parent chainNetGCF_004115215.2Viewchain subGroups view=chain shortLabel platypus rBestChain longLabel platypus (Nov. 2020 GCF_004115215.2_mOrnAna1.pri.v4) Reciprocal Best Chained Alignments type bigChain GCF_004115215.2 bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_004115215.2.bb linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_004115215.2Link.bb track mafNetGCF_004115215.2Viewnet shortLabel Net view net visibility full parent chainNetGCF_004115215.2 track netGCF_004115215.2 parent mafNetGCF_004115215.2Viewnet subGroups view=net shortLabel platypus mafNet longLabel platypus (Nov. 2020 GCF_004115215.2_mOrnAna1.pri.v4) mafNet Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_004115215.2.net.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_004115215.2.net.summary.bb speciesOrder GCF_004115215.2 speciesLabels GCF_004115215.2="platypus" track synNetGCF_004115215.2 parent mafNetGCF_004115215.2Viewnet subGroups view=net shortLabel platypus synNet longLabel platypus (Nov. 2020 GCF_004115215.2_mOrnAna1.pri.v4) Syntenic Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_004115215.2.synNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_004115215.2.synNet.summary.bb speciesOrder GCF_004115215.2 speciesLabels GCF_004115215.2="platypus" track rbestNetGCF_004115215.2 parent mafNetGCF_004115215.2Viewnet subGroups view=net shortLabel platypus rBestNet longLabel platypus (Nov. 2020 GCF_004115215.2_mOrnAna1.pri.v4) Reciprocal Best Net Alignment type bigMaf bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_004115215.2.rbestNet.bb summary /gbdb/$D/bbi/chainNet/$D.GCF_004115215.2.rbestNet.summary.bb speciesOrder GCF_004115215.2 speciesLabels GCF_004115215.2="platypus" ############################################################################## + +############################################################################## +# GCA_018873775.2 - human - Homo sapiens - taxId: 9606 - primates +############################################################################## +track chainNetGCA_018873775.2 +compositeTrack on +shortLabel HG01243.v3.0 Chain/Net +longLabel human (Sep. 2021 GCA_018873775.2_hg01243.v3.0), Chain and Net Alignments +subGroup1 view Views chain=Chain net=Net +dragAndDrop subTracks +visibility hide +group compGeno +noInherit on +priority 100.1 +color 0,0,0 +altColor 100,50,0 +type bed 3 +sortOrder view=+ +matrix 16 90,-330,-236,-356,-330,100,-318,-236,-236,-318,100,-330,-356,-236,-330,90 +chainMinScore 5000 +chainLinearGap medium +matrixHeader A, C, G, T +otherDb GCA_018873775.2 +html chainNet + + track chainNetGCA_018873775.2Viewchain + shortLabel Chain + view chain + visibility pack + parent chainNetGCA_018873775.2 + spectrum on + + track chainGCA_018873775.2 + parent chainNetGCA_018873775.2Viewchain + subGroups view=chain + shortLabel human Chain + longLabel human (Sep. 2021 GCA_018873775.2_hg01243.v3.0) Chained Alignments + type bigChain GCA_018873775.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainGCA_018873775.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainGCA_018873775.2Link.bb + + track chainSynGCA_018873775.2 + parent chainNetGCA_018873775.2Viewchain + subGroups view=chain + shortLabel human synChain + longLabel human (Sep. 2021 GCA_018873775.2_hg01243.v3.0) Syntenic Chained Alignments + type bigChain GCA_018873775.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainSynGCA_018873775.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainSynGCA_018873775.2Link.bb + + track chainRBestGCA_018873775.2 + parent chainNetGCA_018873775.2Viewchain + subGroups view=chain + shortLabel human rBestChain + longLabel human (Sep. 2021 GCA_018873775.2_hg01243.v3.0) Reciprocal Best Chained Alignments + type bigChain GCA_018873775.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainRBestGCA_018873775.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainRBestGCA_018873775.2Link.bb + + track mafNetGCA_018873775.2Viewnet + shortLabel Net + view net + visibility full + parent chainNetGCA_018873775.2 + + track netGCA_018873775.2 + parent mafNetGCA_018873775.2Viewnet + subGroups view=net + shortLabel human mafNet + longLabel human (Sep. 2021 GCA_018873775.2_hg01243.v3.0) mafNet Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_018873775.2.net.bb + summary /gbdb/$D/chainNet/$D.GCA_018873775.2.net.summary.bb + speciesOrder GCA_018873775.2 + speciesLabels GCA_018873775.2="human" + + track synNetGCA_018873775.2 + parent mafNetGCA_018873775.2Viewnet + subGroups view=net + shortLabel human synNet + longLabel human (Sep. 2021 GCA_018873775.2_hg01243.v3.0) Syntenic Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_018873775.2.synNet.bb + summary /gbdb/$D/chainNet/$D.GCA_018873775.2.synNet.summary.bb + speciesOrder GCA_018873775.2 + speciesLabels GCA_018873775.2="human" + + track rbestNetGCA_018873775.2 + parent mafNetGCA_018873775.2Viewnet + subGroups view=net + shortLabel human rBestNet + longLabel human (Sep. 2021 GCA_018873775.2_hg01243.v3.0) Reciprocal Best Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_018873775.2.rbestNet.bb + summary /gbdb/$D/chainNet/$D.GCA_018873775.2.rbestNet.summary.bb + speciesOrder GCA_018873775.2 + speciesLabels GCA_018873775.2="human" +