464078525816d376c389e73c283e0ee40b6d0f2b hiram Mon Apr 22 21:36:46 2024 -0700 add a number of T2T primates no redmine diff --git src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra index ac2abf7..ead4c2a 100644 --- src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra +++ src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra @@ -1,15 +1,209 @@ +############################################################################## +# GCA_029289425.2 - pygmy chimpanzee - Pan paniscus - taxId: 9597 - primates +############################################################################## +track chainNetGCA_029289425.2 +compositeTrack on +shortLabel pygmy chimpanzee Chain/Net +longLabel pygmy chimpanzee (Jan. 2024 GCA_029289425.2_NHGRI_mPanPan1-v2.0_pri), Chain and Net Alignments +subGroup1 view Views chain=Chain net=Net +dragAndDrop subTracks +visibility hide +group compGeno +noInherit on +priority 496 +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_029289425.2 +html chainNet + + track chainNetGCA_029289425.2Viewchain + shortLabel Chain + view chain + visibility pack + parent chainNetGCA_029289425.2 + spectrum on + + track chainGCA_029289425.2 + parent chainNetGCA_029289425.2Viewchain + subGroups view=chain + shortLabel pygmy chimpanzee Chain + longLabel pygmy chimpanzee (Jan. 2024 GCA_029289425.2_NHGRI_mPanPan1-v2.0_pri) Chained Alignments + type bigChain GCA_029289425.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainGCA_029289425.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainGCA_029289425.2Link.bb + + track chainSynGCA_029289425.2 + parent chainNetGCA_029289425.2Viewchain + subGroups view=chain + shortLabel pygmy chimpanzee synChain + longLabel pygmy chimpanzee (Jan. 2024 GCA_029289425.2_NHGRI_mPanPan1-v2.0_pri) Syntenic Chained Alignments + type bigChain GCA_029289425.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainSynGCA_029289425.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainSynGCA_029289425.2Link.bb + + track chainRBestGCA_029289425.2 + parent chainNetGCA_029289425.2Viewchain + subGroups view=chain + shortLabel pygmy chimpanzee rBestChain + longLabel pygmy chimpanzee (Jan. 2024 GCA_029289425.2_NHGRI_mPanPan1-v2.0_pri) Reciprocal Best Chained Alignments + type bigChain GCA_029289425.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainRBestGCA_029289425.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainRBestGCA_029289425.2Link.bb + + track mafNetGCA_029289425.2Viewnet + shortLabel Net + view net + visibility full + parent chainNetGCA_029289425.2 + + track netGCA_029289425.2 + parent mafNetGCA_029289425.2Viewnet + subGroups view=net + shortLabel pygmy chimpanzee mafNet + longLabel pygmy chimpanzee (Jan. 2024 GCA_029289425.2_NHGRI_mPanPan1-v2.0_pri) mafNet Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_029289425.2.net.bb + summary /gbdb/$D/chainNet/$D.GCA_029289425.2.net.summary.bb + speciesOrder GCA_029289425.2 + speciesLabels GCA_029289425.2="pygmy chimpanzee" + + track synNetGCA_029289425.2 + parent mafNetGCA_029289425.2Viewnet + subGroups view=net + shortLabel pygmy chimpanzee synNet + longLabel pygmy chimpanzee (Jan. 2024 GCA_029289425.2_NHGRI_mPanPan1-v2.0_pri) Syntenic Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_029289425.2.synNet.bb + summary /gbdb/$D/chainNet/$D.GCA_029289425.2.synNet.summary.bb + speciesOrder GCA_029289425.2 + speciesLabels GCA_029289425.2="pygmy chimpanzee" + + track rbestNetGCA_029289425.2 + parent mafNetGCA_029289425.2Viewnet + subGroups view=net + shortLabel pygmy chimpanzee rBestNet + longLabel pygmy chimpanzee (Jan. 2024 GCA_029289425.2_NHGRI_mPanPan1-v2.0_pri) Reciprocal Best Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_029289425.2.rbestNet.bb + summary /gbdb/$D/chainNet/$D.GCA_029289425.2.rbestNet.summary.bb + speciesOrder GCA_029289425.2 + speciesLabels GCA_029289425.2="pygmy chimpanzee" + +############################################################################## +# GCA_028858775.2 - chimpanzee - Pan troglodytes - taxId: 9598 - primates +############################################################################## +track chainNetGCA_028858775.2 +compositeTrack on +shortLabel chimpanzee Chain/Net +longLabel chimpanzee (Jan. 2024 GCA_028858775.2_NHGRI_mPanTro3-v2.0_pri), Chain and Net Alignments +subGroup1 view Views chain=Chain net=Net +dragAndDrop subTracks +visibility hide +group compGeno +noInherit on +priority 497 +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_028858775.2 +html chainNet + + track chainNetGCA_028858775.2Viewchain + shortLabel Chain + view chain + visibility pack + parent chainNetGCA_028858775.2 + spectrum on + + track chainGCA_028858775.2 + parent chainNetGCA_028858775.2Viewchain + subGroups view=chain + shortLabel chimpanzee Chain + longLabel chimpanzee (Jan. 2024 GCA_028858775.2_NHGRI_mPanTro3-v2.0_pri) Chained Alignments + type bigChain GCA_028858775.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainGCA_028858775.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainGCA_028858775.2Link.bb + + track chainSynGCA_028858775.2 + parent chainNetGCA_028858775.2Viewchain + subGroups view=chain + shortLabel chimpanzee synChain + longLabel chimpanzee (Jan. 2024 GCA_028858775.2_NHGRI_mPanTro3-v2.0_pri) Syntenic Chained Alignments + type bigChain GCA_028858775.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainSynGCA_028858775.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainSynGCA_028858775.2Link.bb + + track chainRBestGCA_028858775.2 + parent chainNetGCA_028858775.2Viewchain + subGroups view=chain + shortLabel chimpanzee rBestChain + longLabel chimpanzee (Jan. 2024 GCA_028858775.2_NHGRI_mPanTro3-v2.0_pri) Reciprocal Best Chained Alignments + type bigChain GCA_028858775.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainRBestGCA_028858775.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainRBestGCA_028858775.2Link.bb + + track mafNetGCA_028858775.2Viewnet + shortLabel Net + view net + visibility full + parent chainNetGCA_028858775.2 + + track netGCA_028858775.2 + parent mafNetGCA_028858775.2Viewnet + subGroups view=net + shortLabel chimpanzee mafNet + longLabel chimpanzee (Jan. 2024 GCA_028858775.2_NHGRI_mPanTro3-v2.0_pri) mafNet Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_028858775.2.net.bb + summary /gbdb/$D/chainNet/$D.GCA_028858775.2.net.summary.bb + speciesOrder GCA_028858775.2 + speciesLabels GCA_028858775.2="chimpanzee" + + track synNetGCA_028858775.2 + parent mafNetGCA_028858775.2Viewnet + subGroups view=net + shortLabel chimpanzee synNet + longLabel chimpanzee (Jan. 2024 GCA_028858775.2_NHGRI_mPanTro3-v2.0_pri) Syntenic Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_028858775.2.synNet.bb + summary /gbdb/$D/chainNet/$D.GCA_028858775.2.synNet.summary.bb + speciesOrder GCA_028858775.2 + speciesLabels GCA_028858775.2="chimpanzee" + + track rbestNetGCA_028858775.2 + parent mafNetGCA_028858775.2Viewnet + subGroups view=net + shortLabel chimpanzee rBestNet + longLabel chimpanzee (Jan. 2024 GCA_028858775.2_NHGRI_mPanTro3-v2.0_pri) Reciprocal Best Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_028858775.2.rbestNet.bb + summary /gbdb/$D/chainNet/$D.GCA_028858775.2.rbestNet.summary.bb + speciesOrder GCA_028858775.2 + speciesLabels GCA_028858775.2="chimpanzee" + ################################################################ # panTro6 - chimp - Pan troglodytes - primate - taxId 9598 ################################################################ track chainNetPanTro6 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 498 color 0,0,0 altColor 100,50,0 @@ -622,30 +816,127 @@ track chainNetRheMac1Viewnet shortLabel Net view net visibility full parent chainNetRheMac1 track netRheMac1 parent chainNetRheMac1Viewnet subGroups view=net shortLabel $o_db Net longLabel $o_Organism ($o_date) Alignment net type netAlign rheMac1 chainRheMac1 html chainNet +############################################################################## +# GCA_029281585.2 - western lowland gorilla - Gorilla gorilla gorilla - taxId: 9595 - primates +############################################################################## +track chainNetGCA_029281585.2 +compositeTrack on +shortLabel western lowland gorilla Chain/Net +longLabel western lowland gorilla (Jan. 2024 GCA_029281585.2_NHGRI_mGorGor1-v2.0_pri), Chain and Net Alignments +subGroup1 view Views chain=Chain net=Net +dragAndDrop subTracks +visibility hide +group compGeno +noInherit on +priority 220.2 +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_029281585.2 +html chainNet + + track chainNetGCA_029281585.2Viewchain + shortLabel Chain + view chain + visibility pack + parent chainNetGCA_029281585.2 + spectrum on + + track chainGCA_029281585.2 + parent chainNetGCA_029281585.2Viewchain + subGroups view=chain + shortLabel western lowland gorilla Chain + longLabel western lowland gorilla (Jan. 2024 GCA_029281585.2_NHGRI_mGorGor1-v2.0_pri) Chained Alignments + type bigChain GCA_029281585.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainGCA_029281585.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainGCA_029281585.2Link.bb + + track chainSynGCA_029281585.2 + parent chainNetGCA_029281585.2Viewchain + subGroups view=chain + shortLabel western lowland gorilla synChain + longLabel western lowland gorilla (Jan. 2024 GCA_029281585.2_NHGRI_mGorGor1-v2.0_pri) Syntenic Chained Alignments + type bigChain GCA_029281585.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainSynGCA_029281585.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainSynGCA_029281585.2Link.bb + + track chainRBestGCA_029281585.2 + parent chainNetGCA_029281585.2Viewchain + subGroups view=chain + shortLabel western lowland gorilla rBestChain + longLabel western lowland gorilla (Jan. 2024 GCA_029281585.2_NHGRI_mGorGor1-v2.0_pri) Reciprocal Best Chained Alignments + type bigChain GCA_029281585.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainRBestGCA_029281585.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainRBestGCA_029281585.2Link.bb + + track mafNetGCA_029281585.2Viewnet + shortLabel Net + view net + visibility full + parent chainNetGCA_029281585.2 + + track netGCA_029281585.2 + parent mafNetGCA_029281585.2Viewnet + subGroups view=net + shortLabel western lowland gorilla mafNet + longLabel western lowland gorilla (Jan. 2024 GCA_029281585.2_NHGRI_mGorGor1-v2.0_pri) mafNet Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_029281585.2.net.bb + summary /gbdb/$D/chainNet/$D.GCA_029281585.2.net.summary.bb + speciesOrder GCA_029281585.2 + speciesLabels GCA_029281585.2="western lowland gorilla" + + track synNetGCA_029281585.2 + parent mafNetGCA_029281585.2Viewnet + subGroups view=net + shortLabel western lowland gorilla synNet + longLabel western lowland gorilla (Jan. 2024 GCA_029281585.2_NHGRI_mGorGor1-v2.0_pri) Syntenic Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_029281585.2.synNet.bb + summary /gbdb/$D/chainNet/$D.GCA_029281585.2.synNet.summary.bb + speciesOrder GCA_029281585.2 + speciesLabels GCA_029281585.2="western lowland gorilla" + + track rbestNetGCA_029281585.2 + parent mafNetGCA_029281585.2Viewnet + subGroups view=net + shortLabel western lowland gorilla rBestNet + longLabel western lowland gorilla (Jan. 2024 GCA_029281585.2_NHGRI_mGorGor1-v2.0_pri) Reciprocal Best Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_029281585.2.rbestNet.bb + summary /gbdb/$D/chainNet/$D.GCA_029281585.2.rbestNet.summary.bb + speciesOrder GCA_029281585.2 + speciesLabels GCA_029281585.2="western lowland gorilla" + ################################################################ # gorGor6 - Gorilla - Gorilla gorilla - primate ################################################################ track chainNetGorGor6 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 220.3 color 0,0,0 altColor 100,50,0 @@ -940,30 +1231,226 @@ track chainNetGorGor1Viewnet shortLabel Net view net visibility full parent chainNetGorGor1 track netGorGor1 parent chainNetGorGor1Viewnet subGroups view=net shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment net type netAlign gorGor1 chainGorGor1 html chainNet +############################################################################## +# GCA_028885625.2 - Bornean orangutan - Pongo pygmaeus - taxId: 9600 - primates +############################################################################## +track chainNetGCA_028885625.2 +compositeTrack on +shortLabel Bornean orangutan Chain/Net +longLabel Bornean orangutan (Jan. 2024 GCA_028885625.2_NHGRI_mPonPyg2-v2.0_pri), Chain and Net Alignments +subGroup1 view Views chain=Chain net=Net +dragAndDrop subTracks +visibility hide +group compGeno +noInherit on +priority 496 +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_028885625.2 +html chainNet + + track chainNetGCA_028885625.2Viewchain + shortLabel Chain + view chain + visibility pack + parent chainNetGCA_028885625.2 + spectrum on + + track chainGCA_028885625.2 + parent chainNetGCA_028885625.2Viewchain + subGroups view=chain + shortLabel Bornean orangutan Chain + longLabel Bornean orangutan (Jan. 2024 GCA_028885625.2_NHGRI_mPonPyg2-v2.0_pri) Chained Alignments + type bigChain GCA_028885625.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainGCA_028885625.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainGCA_028885625.2Link.bb + + track chainSynGCA_028885625.2 + parent chainNetGCA_028885625.2Viewchain + subGroups view=chain + shortLabel Bornean orangutan synChain + longLabel Bornean orangutan (Jan. 2024 GCA_028885625.2_NHGRI_mPonPyg2-v2.0_pri) Syntenic Chained Alignments + type bigChain GCA_028885625.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainSynGCA_028885625.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainSynGCA_028885625.2Link.bb + + track chainRBestGCA_028885625.2 + parent chainNetGCA_028885625.2Viewchain + subGroups view=chain + shortLabel Bornean orangutan rBestChain + longLabel Bornean orangutan (Jan. 2024 GCA_028885625.2_NHGRI_mPonPyg2-v2.0_pri) Reciprocal Best Chained Alignments + type bigChain GCA_028885625.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainRBestGCA_028885625.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainRBestGCA_028885625.2Link.bb + + track mafNetGCA_028885625.2Viewnet + shortLabel Net + view net + visibility full + parent chainNetGCA_028885625.2 + + track netGCA_028885625.2 + parent mafNetGCA_028885625.2Viewnet + subGroups view=net + shortLabel Bornean orangutan mafNet + longLabel Bornean orangutan (Jan. 2024 GCA_028885625.2_NHGRI_mPonPyg2-v2.0_pri) mafNet Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_028885625.2.net.bb + summary /gbdb/$D/chainNet/$D.GCA_028885625.2.net.summary.bb + speciesOrder GCA_028885625.2 + speciesLabels GCA_028885625.2="Bornean orangutan" + + track synNetGCA_028885625.2 + parent mafNetGCA_028885625.2Viewnet + subGroups view=net + shortLabel Bornean orangutan synNet + longLabel Bornean orangutan (Jan. 2024 GCA_028885625.2_NHGRI_mPonPyg2-v2.0_pri) Syntenic Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_028885625.2.synNet.bb + summary /gbdb/$D/chainNet/$D.GCA_028885625.2.synNet.summary.bb + speciesOrder GCA_028885625.2 + speciesLabels GCA_028885625.2="Bornean orangutan" + + track rbestNetGCA_028885625.2 + parent mafNetGCA_028885625.2Viewnet + subGroups view=net + shortLabel Bornean orangutan rBestNet + longLabel Bornean orangutan (Jan. 2024 GCA_028885625.2_NHGRI_mPonPyg2-v2.0_pri) Reciprocal Best Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_028885625.2.rbestNet.bb + summary /gbdb/$D/chainNet/$D.GCA_028885625.2.rbestNet.summary.bb + speciesOrder GCA_028885625.2 + speciesLabels GCA_028885625.2="Bornean orangutan" + + +############################################################################## +# GCA_028885655.2 - Sumatran orangutan - Pongo abelii - taxId: 9601 - primates +############################################################################## +track chainNetGCA_028885655.2 +compositeTrack on +shortLabel Sumatran orangutan Chain/Net +longLabel Sumatran orangutan (Jan. 2024 GCA_028885655.2_NHGRI_mPonAbe1-v2.0_pri), Chain and Net Alignments +subGroup1 view Views chain=Chain net=Net +dragAndDrop subTracks +visibility hide +group compGeno +noInherit on +priority 497 +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_028885655.2 +html chainNet + + track chainNetGCA_028885655.2Viewchain + shortLabel Chain + view chain + visibility pack + parent chainNetGCA_028885655.2 + spectrum on + + track chainGCA_028885655.2 + parent chainNetGCA_028885655.2Viewchain + subGroups view=chain + shortLabel Sumatran orangutan Chain + longLabel Sumatran orangutan (Jan. 2024 GCA_028885655.2_NHGRI_mPonAbe1-v2.0_pri) Chained Alignments + type bigChain GCA_028885655.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainGCA_028885655.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainGCA_028885655.2Link.bb + + track chainSynGCA_028885655.2 + parent chainNetGCA_028885655.2Viewchain + subGroups view=chain + shortLabel Sumatran orangutan synChain + longLabel Sumatran orangutan (Jan. 2024 GCA_028885655.2_NHGRI_mPonAbe1-v2.0_pri) Syntenic Chained Alignments + type bigChain GCA_028885655.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainSynGCA_028885655.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainSynGCA_028885655.2Link.bb + + track chainRBestGCA_028885655.2 + parent chainNetGCA_028885655.2Viewchain + subGroups view=chain + shortLabel Sumatran orangutan rBestChain + longLabel Sumatran orangutan (Jan. 2024 GCA_028885655.2_NHGRI_mPonAbe1-v2.0_pri) Reciprocal Best Chained Alignments + type bigChain GCA_028885655.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainRBestGCA_028885655.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainRBestGCA_028885655.2Link.bb + + track mafNetGCA_028885655.2Viewnet + shortLabel Net + view net + visibility full + parent chainNetGCA_028885655.2 + + track netGCA_028885655.2 + parent mafNetGCA_028885655.2Viewnet + subGroups view=net + shortLabel Sumatran orangutan mafNet + longLabel Sumatran orangutan (Jan. 2024 GCA_028885655.2_NHGRI_mPonAbe1-v2.0_pri) mafNet Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_028885655.2.net.bb + summary /gbdb/$D/chainNet/$D.GCA_028885655.2.net.summary.bb + speciesOrder GCA_028885655.2 + speciesLabels GCA_028885655.2="Sumatran orangutan" + + track synNetGCA_028885655.2 + parent mafNetGCA_028885655.2Viewnet + subGroups view=net + shortLabel Sumatran orangutan synNet + longLabel Sumatran orangutan (Jan. 2024 GCA_028885655.2_NHGRI_mPonAbe1-v2.0_pri) Syntenic Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_028885655.2.synNet.bb + summary /gbdb/$D/chainNet/$D.GCA_028885655.2.synNet.summary.bb + speciesOrder GCA_028885655.2 + speciesLabels GCA_028885655.2="Sumatran orangutan" + + track rbestNetGCA_028885655.2 + parent mafNetGCA_028885655.2Viewnet + subGroups view=net + shortLabel Sumatran orangutan rBestNet + longLabel Sumatran orangutan (Jan. 2024 GCA_028885655.2_NHGRI_mPonAbe1-v2.0_pri) Reciprocal Best Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_028885655.2.rbestNet.bb + summary /gbdb/$D/chainNet/$D.GCA_028885655.2.rbestNet.summary.bb + speciesOrder GCA_028885655.2 + speciesLabels GCA_028885655.2="Sumatran orangutan" + + ################################################################ # ponAbe3 - Bonobo - Pongo pygmaeus abelii - primate - taxId 9601 ################################################################ track chainNetPonAbe3 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 498 color 0,0,0 altColor 100,50,0 @@ -2120,30 +2607,422 @@ track chainNetProCoq1Viewnet shortLabel Net view net visibility full parent chainNetProCoq1 track netProCoq1 parent chainNetProCoq1Viewnet subGroups view=net shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment net type netAlign proCoq1 chainProCoq1 html chainNet +############################################################################## +# GCA_028878055.2 - siamang - Symphalangus syndactylus - taxId: 9590 - primates +############################################################################## +track chainNetGCA_028878055.2 +compositeTrack on +shortLabel siamang Chain/Net +longLabel siamang (Jan. 2024 GCA_028878055.2_NHGRI_mSymSyn1-v2.0_pri), Chain and Net Alignments +subGroup1 view Views chain=Chain net=Net +dragAndDrop subTracks +visibility hide +group compGeno +noInherit on +priority 260.0 +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_028878055.2 +html chainNet + + track chainNetGCA_028878055.2Viewchain + shortLabel Chain + view chain + visibility pack + parent chainNetGCA_028878055.2 + spectrum on + + track chainGCA_028878055.2 + parent chainNetGCA_028878055.2Viewchain + subGroups view=chain + shortLabel siamang Chain + longLabel siamang (Jan. 2024 GCA_028878055.2_NHGRI_mSymSyn1-v2.0_pri) Chained Alignments + type bigChain GCA_028878055.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainGCA_028878055.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainGCA_028878055.2Link.bb + + track chainSynGCA_028878055.2 + parent chainNetGCA_028878055.2Viewchain + subGroups view=chain + shortLabel siamang synChain + longLabel siamang (Jan. 2024 GCA_028878055.2_NHGRI_mSymSyn1-v2.0_pri) Syntenic Chained Alignments + type bigChain GCA_028878055.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainSynGCA_028878055.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainSynGCA_028878055.2Link.bb + + track chainRBestGCA_028878055.2 + parent chainNetGCA_028878055.2Viewchain + subGroups view=chain + shortLabel siamang rBestChain + longLabel siamang (Jan. 2024 GCA_028878055.2_NHGRI_mSymSyn1-v2.0_pri) Reciprocal Best Chained Alignments + type bigChain GCA_028878055.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainRBestGCA_028878055.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainRBestGCA_028878055.2Link.bb + + track mafNetGCA_028878055.2Viewnet + shortLabel Net + view net + visibility full + parent chainNetGCA_028878055.2 + + track netGCA_028878055.2 + parent mafNetGCA_028878055.2Viewnet + subGroups view=net + shortLabel siamang mafNet + longLabel siamang (Jan. 2024 GCA_028878055.2_NHGRI_mSymSyn1-v2.0_pri) mafNet Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_028878055.2.net.bb + summary /gbdb/$D/chainNet/$D.GCA_028878055.2.net.summary.bb + speciesOrder GCA_028878055.2 + speciesLabels GCA_028878055.2="siamang" + + track synNetGCA_028878055.2 + parent mafNetGCA_028878055.2Viewnet + subGroups view=net + shortLabel siamang synNet + longLabel siamang (Jan. 2024 GCA_028878055.2_NHGRI_mSymSyn1-v2.0_pri) Syntenic Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_028878055.2.synNet.bb + summary /gbdb/$D/chainNet/$D.GCA_028878055.2.synNet.summary.bb + speciesOrder GCA_028878055.2 + speciesLabels GCA_028878055.2="siamang" + + track rbestNetGCA_028878055.2 + parent mafNetGCA_028878055.2Viewnet + subGroups view=net + shortLabel siamang rBestNet + longLabel siamang (Jan. 2024 GCA_028878055.2_NHGRI_mSymSyn1-v2.0_pri) Reciprocal Best Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCA_028878055.2.rbestNet.bb + summary /gbdb/$D/chainNet/$D.GCA_028878055.2.rbestNet.summary.bb + speciesOrder GCA_028878055.2 + speciesLabels GCA_028878055.2="siamang" + + +############################################################################## +# GCF_020740605.2 - Ring-tailed lemur - Lemur catta - taxId: 9447 - primates +############################################################################## +track chainNetGCF_020740605.2 +compositeTrack on +shortLabel Ring-tailed lemur Chain/Net +longLabel Ring-tailed lemur (Nov. 2021 GCF_020740605.2_mLemCat1.pri), Chain and Net Alignments +subGroup1 view Views chain=Chain net=Net +dragAndDrop subTracks +visibility hide +group compGeno +noInherit on +priority 260.1 +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 GCF_020740605.2 +html chainNet + + track chainNetGCF_020740605.2Viewchain + shortLabel Chain + view chain + visibility pack + parent chainNetGCF_020740605.2 + spectrum on + + track chainGCF_020740605.2 + parent chainNetGCF_020740605.2Viewchain + subGroups view=chain + shortLabel Ring-tailed lemur Chain + longLabel Ring-tailed lemur (Nov. 2021 GCF_020740605.2_mLemCat1.pri) Chained Alignments + type bigChain GCF_020740605.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainGCF_020740605.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainGCF_020740605.2Link.bb + + track chainSynGCF_020740605.2 + parent chainNetGCF_020740605.2Viewchain + subGroups view=chain + shortLabel Ring-tailed lemur synChain + longLabel Ring-tailed lemur (Nov. 2021 GCF_020740605.2_mLemCat1.pri) Syntenic Chained Alignments + type bigChain GCF_020740605.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainSynGCF_020740605.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainSynGCF_020740605.2Link.bb + + track chainRBestGCF_020740605.2 + parent chainNetGCF_020740605.2Viewchain + subGroups view=chain + shortLabel Ring-tailed lemur rBestChain + longLabel Ring-tailed lemur (Nov. 2021 GCF_020740605.2_mLemCat1.pri) Reciprocal Best Chained Alignments + type bigChain GCF_020740605.2 + bigDataUrl /gbdb/$D/chainNet/$D.chainRBestGCF_020740605.2.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainRBestGCF_020740605.2Link.bb + + track mafNetGCF_020740605.2Viewnet + shortLabel Net + view net + visibility full + parent chainNetGCF_020740605.2 + + track netGCF_020740605.2 + parent mafNetGCF_020740605.2Viewnet + subGroups view=net + shortLabel Ring-tailed lemur mafNet + longLabel Ring-tailed lemur (Nov. 2021 GCF_020740605.2_mLemCat1.pri) mafNet Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCF_020740605.2.net.bb + summary /gbdb/$D/chainNet/$D.GCF_020740605.2.net.summary.bb + speciesOrder GCF_020740605.2 + speciesLabels GCF_020740605.2="Ring-tailed lemur" + + track synNetGCF_020740605.2 + parent mafNetGCF_020740605.2Viewnet + subGroups view=net + shortLabel Ring-tailed lemur synNet + longLabel Ring-tailed lemur (Nov. 2021 GCF_020740605.2_mLemCat1.pri) Syntenic Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCF_020740605.2.synNet.bb + summary /gbdb/$D/chainNet/$D.GCF_020740605.2.synNet.summary.bb + speciesOrder GCF_020740605.2 + speciesLabels GCF_020740605.2="Ring-tailed lemur" + + track rbestNetGCF_020740605.2 + parent mafNetGCF_020740605.2Viewnet + subGroups view=net + shortLabel Ring-tailed lemur rBestNet + longLabel Ring-tailed lemur (Nov. 2021 GCF_020740605.2_mLemCat1.pri) Reciprocal Best Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCF_020740605.2.rbestNet.bb + summary /gbdb/$D/chainNet/$D.GCF_020740605.2.rbestNet.summary.bb + speciesOrder GCF_020740605.2 + speciesLabels GCF_020740605.2="Ring-tailed lemur" + + +############################################################################## +# GCF_011100555.1 - white-tufted-ear marmoset - Callithrix jacchus - taxId: 9483 - primates +############################################################################## +track chainNetGCF_011100555.1 +compositeTrack on +shortLabel white-tufted-ear marmoset Chain/Net +longLabel white-tufted-ear marmoset (Apr. 2021 GCF_011100555.1_mCalJa1.2.pat.X), Chain and Net Alignments +subGroup1 view Views chain=Chain net=Net +dragAndDrop subTracks +visibility hide +group compGeno +noInherit on +priority 260.1 +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 GCF_011100555.1 +html chainNet + + track chainNetGCF_011100555.1Viewchain + shortLabel Chain + view chain + visibility pack + parent chainNetGCF_011100555.1 + spectrum on + + track chainGCF_011100555.1 + parent chainNetGCF_011100555.1Viewchain + subGroups view=chain + shortLabel white-tufted-ear marmoset Chain + longLabel white-tufted-ear marmoset (Apr. 2021 GCF_011100555.1_mCalJa1.2.pat.X) Chained Alignments + type bigChain GCF_011100555.1 + bigDataUrl /gbdb/$D/chainNet/$D.chainGCF_011100555.1.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainGCF_011100555.1Link.bb + + track chainSynGCF_011100555.1 + parent chainNetGCF_011100555.1Viewchain + subGroups view=chain + shortLabel white-tufted-ear marmoset synChain + longLabel white-tufted-ear marmoset (Apr. 2021 GCF_011100555.1_mCalJa1.2.pat.X) Syntenic Chained Alignments + type bigChain GCF_011100555.1 + bigDataUrl /gbdb/$D/chainNet/$D.chainSynGCF_011100555.1.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainSynGCF_011100555.1Link.bb + + track chainRBestGCF_011100555.1 + parent chainNetGCF_011100555.1Viewchain + subGroups view=chain + shortLabel white-tufted-ear marmoset rBestChain + longLabel white-tufted-ear marmoset (Apr. 2021 GCF_011100555.1_mCalJa1.2.pat.X) Reciprocal Best Chained Alignments + type bigChain GCF_011100555.1 + bigDataUrl /gbdb/$D/chainNet/$D.chainRBestGCF_011100555.1.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainRBestGCF_011100555.1Link.bb + + track mafNetGCF_011100555.1Viewnet + shortLabel Net + view net + visibility full + parent chainNetGCF_011100555.1 + + track netGCF_011100555.1 + parent mafNetGCF_011100555.1Viewnet + subGroups view=net + shortLabel white-tufted-ear marmoset mafNet + longLabel white-tufted-ear marmoset (Apr. 2021 GCF_011100555.1_mCalJa1.2.pat.X) mafNet Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCF_011100555.1.net.bb + summary /gbdb/$D/chainNet/$D.GCF_011100555.1.net.summary.bb + speciesOrder GCF_011100555.1 + speciesLabels GCF_011100555.1="white-tufted-ear marmoset" + + track synNetGCF_011100555.1 + parent mafNetGCF_011100555.1Viewnet + subGroups view=net + shortLabel white-tufted-ear marmoset synNet + longLabel white-tufted-ear marmoset (Apr. 2021 GCF_011100555.1_mCalJa1.2.pat.X) Syntenic Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCF_011100555.1.synNet.bb + summary /gbdb/$D/chainNet/$D.GCF_011100555.1.synNet.summary.bb + speciesOrder GCF_011100555.1 + speciesLabels GCF_011100555.1="white-tufted-ear marmoset" + + track rbestNetGCF_011100555.1 + parent mafNetGCF_011100555.1Viewnet + subGroups view=net + shortLabel white-tufted-ear marmoset rBestNet + longLabel white-tufted-ear marmoset (Apr. 2021 GCF_011100555.1_mCalJa1.2.pat.X) Reciprocal Best Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCF_011100555.1.rbestNet.bb + summary /gbdb/$D/chainNet/$D.GCF_011100555.1.rbestNet.summary.bb + speciesOrder GCF_011100555.1 + speciesLabels GCF_011100555.1="white-tufted-ear marmoset" + + +############################################################################## +# GCF_027406575.1 - slow loris - Nycticebus coucang - taxId: 9470 - primates +############################################################################## +track chainNetGCF_027406575.1 +compositeTrack on +shortLabel slow loris Chain/Net +longLabel slow loris (Dec. 2022 GCF_027406575.1_mNycCou1.pri), Chain and Net Alignments +subGroup1 view Views chain=Chain net=Net +dragAndDrop subTracks +visibility hide +group compGeno +noInherit on +priority 260.2 +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 GCF_027406575.1 +html chainNet + + track chainNetGCF_027406575.1Viewchain + shortLabel Chain + view chain + visibility pack + parent chainNetGCF_027406575.1 + spectrum on + + track chainGCF_027406575.1 + parent chainNetGCF_027406575.1Viewchain + subGroups view=chain + shortLabel slow loris Chain + longLabel slow loris (Dec. 2022 GCF_027406575.1_mNycCou1.pri) Chained Alignments + type bigChain GCF_027406575.1 + bigDataUrl /gbdb/$D/chainNet/$D.chainGCF_027406575.1.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainGCF_027406575.1Link.bb + + track chainSynGCF_027406575.1 + parent chainNetGCF_027406575.1Viewchain + subGroups view=chain + shortLabel slow loris synChain + longLabel slow loris (Dec. 2022 GCF_027406575.1_mNycCou1.pri) Syntenic Chained Alignments + type bigChain GCF_027406575.1 + bigDataUrl /gbdb/$D/chainNet/$D.chainSynGCF_027406575.1.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainSynGCF_027406575.1Link.bb + + track chainRBestGCF_027406575.1 + parent chainNetGCF_027406575.1Viewchain + subGroups view=chain + shortLabel slow loris rBestChain + longLabel slow loris (Dec. 2022 GCF_027406575.1_mNycCou1.pri) Reciprocal Best Chained Alignments + type bigChain GCF_027406575.1 + bigDataUrl /gbdb/$D/chainNet/$D.chainRBestGCF_027406575.1.bb + linkDataUrl /gbdb/$D/chainNet/$D.chainRBestGCF_027406575.1Link.bb + + track mafNetGCF_027406575.1Viewnet + shortLabel Net + view net + visibility full + parent chainNetGCF_027406575.1 + + track netGCF_027406575.1 + parent mafNetGCF_027406575.1Viewnet + subGroups view=net + shortLabel slow loris mafNet + longLabel slow loris (Dec. 2022 GCF_027406575.1_mNycCou1.pri) mafNet Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCF_027406575.1.net.bb + summary /gbdb/$D/chainNet/$D.GCF_027406575.1.net.summary.bb + speciesOrder GCF_027406575.1 + speciesLabels GCF_027406575.1="slow loris" + + track synNetGCF_027406575.1 + parent mafNetGCF_027406575.1Viewnet + subGroups view=net + shortLabel slow loris synNet + longLabel slow loris (Dec. 2022 GCF_027406575.1_mNycCou1.pri) Syntenic Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCF_027406575.1.synNet.bb + summary /gbdb/$D/chainNet/$D.GCF_027406575.1.synNet.summary.bb + speciesOrder GCF_027406575.1 + speciesLabels GCF_027406575.1="slow loris" + + track rbestNetGCF_027406575.1 + parent mafNetGCF_027406575.1Viewnet + subGroups view=net + shortLabel slow loris rBestNet + longLabel slow loris (Dec. 2022 GCF_027406575.1_mNycCou1.pri) Reciprocal Best Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/chainNet/$D.GCF_027406575.1.rbestNet.bb + summary /gbdb/$D/chainNet/$D.GCF_027406575.1.rbestNet.summary.bb + speciesOrder GCF_027406575.1 + speciesLabels GCF_027406575.1="slow loris" + + ################################################################ # calJac4 - marmoset - Callithrix jacchus - primate - taxId 9483 ################################################################ track chainNetCalJac4 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 260.3 color 0,0,0 altColor 100,50,0