68d6d9b391f13a9f09724ee7943e60ebf1df108b hiram Wed Apr 7 10:07:26 2021 -0700 add definitions for sheep/GCF_002742125.1 rn7 and xenTro10 refs #27321 diff --git src/hg/makeDb/trackDb/human/chainNetPlacental.ra src/hg/makeDb/trackDb/human/chainNetPlacental.ra index bab8b22..f3c5a53 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=RegenRn1 s024b=RegenRn0 s024c=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 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 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 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 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 @@ -263,49 +263,57 @@ subTrack placentalChainNetViewchain off subGroups view=chain species=s022 clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain oryCun1 otherDb oryCun1 track chainPerManBai1 subTrack placentalChainNetViewchain off subGroups view=chain species=s023 clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain perManBai1 otherDb perManBai1 - track chainRegenRn1 + track chainRn7 subTrack placentalChainNetViewchain off subGroups view=chain species=s024a clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments + type chain rn7 + otherDb rn7 + + track chainRegenRn1 + subTrack placentalChainNetViewchain off + subGroups view=chain species=s024b clade=c00 + shortLabel $o_Organism Chain + longLabel $o_Organism ($o_date) Chained Alignments type chain RegenRn1 otherDb regenRn1 track chainRegenRn0 subTrack placentalChainNetViewchain off - subGroups view=chain species=s024b clade=c00 + subGroups view=chain species=s024c clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain RegenRn0 otherDb regenRn0 track chainRn6 subTrack placentalChainNetViewchain off - subGroups view=chain species=s024c clade=c00 + subGroups view=chain species=s024d clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain rn6 otherDb rn6 track chainRn5 subTrack placentalChainNetViewchain off subGroups view=chain species=s025 clade=c00 shortLabel $o_db Chain longLabel $o_Organism ($o_date) Chained Alignments type chain rn5 otherDb rn5 track chainRn4 subTrack placentalChainNetViewchain off @@ -641,49 +649,59 @@ subTrack placentalChainNetViewchain off subGroups view=chain species=s063 clade=c02 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain lipVex1 otherDb lipVex1 track chainOrcOrc1 subTrack placentalChainNetViewchain off subGroups view=chain species=s064 clade=c02 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain orcOrc1 otherDb orcOrc1 - track chainOviAri4 + track chainGCF_002742125.1 subTrack placentalChainNetViewchain off subGroups view=chain species=s065a clade=c02 + 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 + otherDb GCF_002742125.1 + + track chainOviAri4 + subTrack placentalChainNetViewchain off + subGroups view=chain species=s065b clade=c02 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain oviAri4 otherDb oviAri4 track chainOviAri3 subTrack placentalChainNetViewchain off - subGroups view=chain species=s065b clade=c02 + subGroups view=chain species=s065c clade=c02 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain oviAri3 otherDb oviAri3 track chainOviAri1 subTrack placentalChainNetViewchain off - subGroups view=chain species=s065c clade=c02 + subGroups view=chain species=s065d clade=c02 shortLabel $o_db Chain longLabel $o_Organism ($o_date) Chained Alignments type chain oviAri1 otherDb oviAri1 track chainPanHod1 subTrack placentalChainNetViewchain off subGroups view=chain species=s067 clade=c02 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain panHod1 otherDb panHod1 track chainPhyCat1 subTrack placentalChainNetViewchain off @@ -1295,49 +1313,57 @@ subTrack placentalChainNetViewnet off subGroups view=net species=s022 clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign oryCun1 chainOryCun1 otherDb oryCun1 track netPerManBai1 subTrack placentalChainNetViewnet off subGroups view=net species=s023 clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign perManBai1 chainPerManBai1 otherDb perManBai1 - track netRegenRn1 + track netRn7 subTrack placentalChainNetViewnet on subGroups view=net species=s024a clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net + type netAlign rn7 chainRn7 + otherDb rn7 + + track netRegenRn1 + subTrack placentalChainNetViewnet on + subGroups view=net species=s024b clade=c00 + shortLabel $o_Organism Net + longLabel $o_Organism ($o_date) Alignment Net type netAlign regenRn1 chainRegenRn1 otherDb regenRn1 track netRegenRn0 subTrack placentalChainNetViewnet on - subGroups view=net species=s024b clade=c00 + subGroups view=net species=s024c clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign regenRn0 chainRegenRn0 otherDb regenRn0 track netRn6 subTrack placentalChainNetViewnet on - subGroups view=net species=s024c clade=c00 + subGroups view=net species=s024d clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign rn6 chainRn6 otherDb rn6 track netRn5 subTrack placentalChainNetViewnet off subGroups view=net species=s025 clade=c00 shortLabel $o_db Net longLabel $o_Organism ($o_date) Alignment Net type netAlign rn5 chainRn5 otherDb rn5 track netRn4 subTrack placentalChainNetViewnet off @@ -1671,49 +1697,60 @@ subTrack placentalChainNetViewnet off subGroups view=net species=s063 clade=c02 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign lipVex1 chainLipVex1 otherDb lipVex1 track netOrcOrc1 subTrack placentalChainNetViewnet off 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 netOviAri4 + 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 + 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=s065b clade=c02 + subGroups view=net species=s065c clade=c02 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign oviAri3 chainOviAri3 otherDb oviAri3 track netOviAri1 subTrack placentalChainNetViewnet off - subGroups view=net species=s065c clade=c02 + subGroups view=net species=s065d clade=c02 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign oviAri1 chainOviAri1 otherDb oviAri1 track netPanHod1 subTrack placentalChainNetViewnet off subGroups view=net species=s067 clade=c02 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign panHod1 chainPanHod1 otherDb panHod1 track netPhyCat1 subTrack placentalChainNetViewnet off