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/human/chainNetPlacental.ra src/hg/makeDb/trackDb/human/chainNetPlacental.ra index 631bc57..03981cc 100644 --- src/hg/makeDb/trackDb/human/chainNetPlacental.ra +++ src/hg/makeDb/trackDb/human/chainNetPlacental.ra @@ -1,21 +1,21 @@ track placentalChainNet compositeTrack on shortLabel Placental Chain/Net longLabel Non-primate Placental Mammal Genomes, Chain and Net Alignments subGroup1 view Views chain=Chains net=Nets -subGroup2 species Species s000=Guinea_pig s001=Guinea_pig s002=Chinchilla s003=Chinese_hamster s004a=Chinese_hamster_CHOv1 s004b=Chinese_hamster_CHOv2 s004c=RegenCHO1 s005a=Kangaroo_rat s005b=Beaver s006=Malayan_flying_lemur s007=Naked_mole-rat s008=Naked_mole-rat s0081=Damara_mole-rat s009=Lesser_Egyptian_jerboa s010=Golden_hamster s011=Prairie_vole s012a=Mouse s012b=Mouse38B s012c=Mouse s013=Mouse s014=Mouse s015=Mouse s016=Mouse s017=Upper_Galilee_mountains_blind_mole_rat s018=Pika s019=Pika s020=Brush-tailed_rat s021=Rabbit s022=Rabbit s023=Prairie_deer_mouse s024a=Rat s024b=RegenRn1 s024c=RegenRn0 s024d=Rat s025=Rat s026=Rat s027=Rat s028=Rat s029=Squirrel s030=Squirrel s031=Tree_shrew s032=Chinese_tree_shrew s033=Panda s034a=Dog s034b=Dog s034c=Dog s034d=Dog s035=Dog s036=Dog s037=Dog s037b=Cat s038=Cat s039=Cat s040=Cat s041=Cat s042=Weddell_seal s043=Ferret s043a=Southern_sea_otter s044=Hawaiian_monk_seal s045=Pacific_walrus s046=Amur_tiger s047=Polar_bear s048=Minke_whale s049=Bison s050=Wild_yak s051a=Cow s051b=Cow s052=Cow s053=Cow s054=Cow s055=Cow s056=Cow s057=Cow s058=Cow s059=Cow s060=Water_buffalo s061=Bactrian_camel s062=Domestic_goat s063=Yangtze_river_dolphin s064=Killer_whale s065a=Sheep s065b=Sheep s065c=Sheep s065d=Sheep s067=Tibetan_antelope s068=Sperm_whale s069=Pig s070=Pig s071=Pig s072=Pig s073=Dolphin s074=Dolphin s075=Alpaca s076=Alpaca s077=Straw_colored_fruit_bat s078=Big_brown_bat s079=Indian_false_vampire s080=Brandt's_myotis_(bat) s081=David's_myotis_(bat) s082=Microbat s083=Microbat s084=Black_flying-fox s085=Parnell's_mustached_bat s086=Megabat s087=Greater_horseshoe_bat s088=Egyptian_rousette s089=Star-nosed_mole s090=Hedgehog s091=Hedgehog s092=Chinese_pangolin s093=Shrew s094=Shrew s095=White_rhinoceros s096a=Horse s096b=Horse s096c=Horse s098=Przewalski_horse s099=Sloth s100=Armadillo s101=Armadillo s102=Armadillo s103=Cape_golden_mole s104=Tenrec s105=Tenrec s106=Cape_elephant_shrew s107=Elephant s108=Elephant s109=Elephant s110=Aardvark s111=Rock_hyrax s112=Manatee +subGroup2 species Species s000=Guinea_pig s001=Guinea_pig s002=Chinchilla s003=Chinese_hamster s004a=Chinese_hamster_CHOv1 s004b=Chinese_hamster_CHOv2 s004c=RegenCHO1 s005a=Kangaroo_rat s005b=Beaver s006=Malayan_flying_lemur s007=Naked_mole-rat s008=Naked_mole-rat s0081=Damara_mole-rat s009=Lesser_Egyptian_jerboa s010=Golden_hamster s011=Prairie_vole s012a=Mouse s012b=Mouse38B s012c=Mouse s013=Mouse s014=Mouse s015=Mouse s016=Mouse s017=Upper_Galilee_mountains_blind_mole_rat s018=Pika s019=Pika s020=Brush-tailed_rat s021=Rabbit s022=Rabbit s023=Prairie_deer_mouse s024a=Rat s024b=RegenRn1 s024c=RegenRn0 s024d=Rat s025=Rat s026=Rat s027=Rat s028=Rat s029=Squirrel s030=Squirrel s031=Tree_shrew s032=Chinese_tree_shrew s033=Panda s034a=Dog s034b=Dog s034c=Dog s034d=Dog s035=Dog s036=Dog s037=Dog s037b=Cat s038=Cat s039=Cat s040=Cat s041=Cat s042=Weddell_seal s043=Ferret s043a=Southern_sea_otter s044=Hawaiian_monk_seal s045=Pacific_walrus s046=Amur_tiger s047=Polar_bear s048=Minke_whale s049=Bison s050=Wild_yak s051a=Cow s051b=Cow s052=Cow s053=Cow s054=Cow s055=Cow s056=Cow s057=Cow s058=Cow s059=Cow s060=Water_buffalo s061=Bactrian_camel s062=Domestic_goat s063=Yangtze_river_dolphin s064=Killer_whale s065a=Sheep s065b=Sheep s065c=Sheep s065d=Sheep s067=Tibetan_antelope s068=Sperm_whale s069=Pig s070=Pig s071=Pig s072=Pig s073=Dolphin s074=Dolphin s075=Alpaca s076=Alpaca s077=Straw_colored_fruit_bat s078=Big_brown_bat s079=Indian_false_vampire s080=Brandt's_myotis_(bat) s081=David's_myotis_(bat) s082=Microbat s083=Microbat s084=Black_flying-fox s085=Parnell's_mustached_bat s086=Megabat s087=Greater_horseshoe_bat s088=Egyptian_rousette s089=Star-nosed_mole s090=Hedgehog s091=Hedgehog s092=Chinese_pangolin s093=Shrew s094=Shrew s095=White_rhinoceros s096a=Horse s096b=Horse s096c=Horse s098=Przewalski_horse s099=Sloth s100=Armadillo s101=Armadillo s102=Armadillo s103=Cape_golden_mole s104=Tenrec s105=Tenrec s106=Cape_elephant_shrew s107=Elephant s108=Elephant s109a=Asiatic_elephant s109b=Elephant s110=Aardvark s111=Rock_hyrax s112=Manatee subGroup3 clade Clade c00=Euarchontoglires c01=Carnivora c02=Cetartiodactyla c03=Chiroptera c04=Laurasiatheria c05=Perissodactyla c06=Xenarthra c07=Afrotheria dragAndDrop subTracks visibility hide group compGeno noInherit on color 0,0,0 altColor 255,255,0 type bed 3 chainLinearGap loose chainMinScore 5000 dimensions dimensionX=clade dimensionY=species sortOrder species=+ view=+ clade=+ configurable on html placentalChainNet priority 8 @@ -1041,33 +1041,43 @@ subTrack placentalChainNetViewchain off subGroups view=chain species=s107 clade=c07 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain loxAfr3 otherDb loxAfr3 track chainLoxAfr2 subTrack placentalChainNetViewchain off subGroups view=chain species=s108 clade=c07 shortLabel $o_db Chain longLabel $o_Organism ($o_date) Chained Alignments type chain loxAfr2 otherDb loxAfr2 + track chainGCF_024166365.1 + subTrack placentalChainNetViewchain off + subGroups view=chain species=s109a clade=c07 + 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 + otherDb GCF_002742125.1 + track chainLoxAfr1 subTrack placentalChainNetViewchain off - subGroups view=chain species=s109 clade=c07 + subGroups view=chain species=s109b clade=c07 shortLabel $o_db Chain longLabel $o_Organism ($o_date) Chained Alignments type chain loxAfr1 otherDb loxAfr1 track chainOryAfe1 subTrack placentalChainNetViewchain off subGroups view=chain species=s110 clade=c07 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain oryAfe1 otherDb oryAfe1 track chainProCap1 subTrack placentalChainNetViewchain off @@ -1736,30 +1746,31 @@ subGroups view=net species=s064 clade=c02 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign orcOrc1 chainOrcOrc1 otherDb orcOrc1 track netGCF_002742125.1 subTrack placentalChainNetViewnet off subGroups view=net species=s065a clade=c02 shortLabel Rambouillet sheep Net longLabel Rambouillet sheep (Nov. 2017 GCF_002742125.1_Oar_rambouillet_v1.0) Alignment Net 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" itemFirstCharCase noChange track netOviAri4 subTrack placentalChainNetViewnet off subGroups view=net species=s065b clade=c02 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign oviAri4 chainOviAri4 otherDb oviAri4 track netOviAri3 subTrack placentalChainNetViewnet off subGroups view=net species=s065c clade=c02 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net @@ -2106,33 +2117,45 @@ subTrack placentalChainNetViewnet on subGroups view=net species=s107 clade=c07 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign loxAfr3 chainLoxAfr3 otherDb loxAfr3 track netLoxAfr2 subTrack placentalChainNetViewnet off subGroups view=net species=s108 clade=c07 shortLabel $o_db Net longLabel $o_Organism ($o_date) Alignment Net type netAlign loxAfr2 chainLoxAfr2 otherDb loxAfr2 + track netGCF_024166365.1 + subTrack placentalChainNetViewnet off + subGroups view=net species=s109a clade=c07 + 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" + itemFirstCharCase noChange + track netLoxAfr1 subTrack placentalChainNetViewnet off - subGroups view=net species=s109 clade=c07 + subGroups view=net species=s109b clade=c07 shortLabel $o_db Net longLabel $o_Organism ($o_date) Alignment Net type netAlign loxAfr1 chainLoxAfr1 otherDb loxAfr1 track netOryAfe1 subTrack placentalChainNetViewnet off subGroups view=net species=s110 clade=c07 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign oryAfe1 chainOryAfe1 otherDb oryAfe1 track netProCap1 subTrack placentalChainNetViewnet off