3148a2ad3b931f8f9b8412b698ee20a48dd4c391 hiram Tue Aug 23 14:10:38 2022 -0700 adding lastz/chain/net Asiatic elephant GCF_024166365.1 to hg38 per user request refs #29905 diff --git src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra index 19aeb26..e6b6e57 100644 --- src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra +++ src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra @@ -59,51 +59,53 @@ 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 - html chainNet + 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 @@ -119,45 +121,43 @@ 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 - html chainNet 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 - html chainNet ############################################################################## # 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 @@ -174,48 +174,47 @@ 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 - html chainNet 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 - html chainNet + 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 @@ -232,48 +231,47 @@ 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 - html chainNet 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 - html chainNet + 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 @@ -324,51 +322,53 @@ 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 - html chainNet + 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 @@ -385,48 +385,47 @@ 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 - html chainNet 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 - html chainNet + 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 @@ -477,50 +476,53 @@ 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 @@ -571,35 +573,137 @@ 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 - mammal +############################################################################## +track chainNetGCF_024166365.1 +compositeTrack on +shortLabel Asiatic elephant Chain/Net +longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp), 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_haplotyp) 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 Chain + longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp) 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 Chain + longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp) 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_haplotyp) 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 mafNet + longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp) 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 mafNet + longLabel Asiatic elephant (Jul. 2022 GCF_024166365.1_mEleMax1_primary_haplotyp) 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" + +##############################################################################