7b52d31632f9b473eba9939d2d30ce703e401553 hiram Fri Oct 29 15:58:44 2021 -0700 lastz chainNet on GCF_002742125.1 Ramboullet sheep refs #28409 diff --git src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra index cf0a235..3b96459 100644 --- src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra +++ src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra @@ -1,473 +1,510 @@ ############################################################################## # 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 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 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 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 ############################################################################## # 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 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 ############################################################################## # 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/$D/bbi/chainNet/chainGCF_002742125.1.bb - linkDataUrl /gbdb/$D/bbi/chainNet/chainGCF_002742125.1Link.bb - html chainNet + 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 html chainNet + 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 + + 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 + ############################################################################## # 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 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 ############################################################################## # 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 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 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 ############################################################################## # 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_000349665.1.Link.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_000349665.1.Link.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_000349665.1.Link.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 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 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