Mercurial > repos > iuc > hyphy_summary
comparison test-data/fade-out1.json @ 0:f304c108aa1f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
author | iuc |
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date | Wed, 09 Jun 2021 07:03:54 +0000 |
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-1:000000000000 | 0:f304c108aa1f |
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1 { | |
2 "MLE":{ | |
3 "content":{ | |
4 "A":{ | |
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385 }, | |
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1340 }, | |
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1830 [0.8602971535473026, 4.743729967908412, 0.9479345393221196, 1.027828984672408], | |
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1864 [3.047039140343488, 4.608145593146393, 0.9474348583243518, 1.017521860509917], | |
1865 [1.290700280873957, 9.54572882593588, 0.9702226814553423, 1.839407972984919], | |
1866 [2.509179850660672, 5.373942133433619, 0.9582360514879859, 1.295278577458708], | |
1867 [1.063901048033218, 4.674690733751121, 0.9477351731467829, 1.02369294710936], | |
1868 [2.417868325445236, 4.59549424286351, 0.9474612208528058, 1.018060752183956], | |
1869 [4.913788985272692, 3.467629377588986, 0.942681406176089, 0.9284566727271125], | |
1870 [1.429007854908218, 3.614301219742001, 0.9452145077346803, 0.9739956984234311], | |
1871 [0.836698475961197, 4.869344224571774, 0.9482031356339117, 1.033451609269997], | |
1872 [0.5262152299765583, 5.088346633645926, 0.948714794505043, 1.044325304766487], | |
1873 [1.960793333763621, 5.71912057917563, 0.9503758999093366, 1.08117252035229], | |
1874 [0.7732097631693891, 1.584076448708799, 0.9390622317690227, 0.869961548410347], | |
1875 [0.9195650708950849, 5.044317773399662, 0.9485827221964971, 1.041497803439468], | |
1876 [1.381708080244398, 3.476048906177453, 0.9450991204886682, 0.9718299641664154], | |
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1878 [1.328378493092375, 3.33816654990299, 0.9443995340385112, 0.9588917038603108], | |
1879 [1.71386530290558, 3.849657912275591, 0.9457094506316561, 0.9833898490558997], | |
1880 [0.688038154834706, 4.899218010047888, 0.9483402582550097, 1.036344590621631], | |
1881 [1.167653512528822, 4.613153812098028, 0.9475638416335188, 1.020163642879384], | |
1882 [0.929044347689485, 1.712413129970971, 0.9388116146788484, 0.8661671111707], | |
1883 [3.928647484965764, 4.22671622622723, 0.9462571329594913, 0.9939866771352854], | |
1884 [0.9378522946406753, 3.779390287753592, 0.9457796078117342, 0.9847353297231051], | |
1885 [4.213146963569278, 6.505052973373631, 0.9524994128555425, 1.132030080261438], | |
1886 [0.6564982400755376, 0.8830099001810239, 0.9326498757152273, 0.7817582327188448], | |
1887 [0.5480427573431782, 5.064565051462152, 0.9486676226128975, 1.043313743837275], | |
1888 [0.9874024301563478, 4.950446146392183, 0.9461037373382979, 0.9909969902335249], | |
1889 [0.915423961533828, 4.715052718414841, 0.94785703090977, 1.026217242398191], | |
1890 [0.3599690382446046, 5.263283051514461, 0.9397199297273854, 0.8800693900086873], | |
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1892 [0.3510396695955084, 5.273501390735112, 0.9392631837888819, 0.8730266582108971], | |
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1894 [0.6025120210968949, 4.968900433897946, 0.948471794582736, 1.039134182648084], | |
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1898 [0.6666015318274037, 3.927601784630151, 0.9461694441223355, 0.9922755320135657], | |
1899 [1.131605370904652, 4.630644791967605, 0.9476401812238463, 1.021733329845507], | |
1900 [1.034003395584375, 4.421573918310028, 0.9471808655051942, 1.012357404922071], | |
1901 [0.7851536508405906, 4.825849766907228, 0.9481540373233673, 1.032419465098889], | |
1902 [3.233252354267688, 3.722746249019892, 0.9450444360182146, 0.9708067530067481], | |
1903 [0.8631584981646886, 1.751514361445709, 0.9396507461491469, 0.87899577247919], | |
1904 [1.3138650589674, 4.593814388489005, 0.9474896539697347, 1.018642576466122], | |
1905 [0.9874024301563478, 4.950446146392183, 0.9461037373382979, 0.9909969902335249], | |
1906 [0.9389062657947818, 4.71394749250261, 0.9478368936632424, 1.025799283945789], | |
1907 [0.6332554271500554, 4.882149770507418, 0.9483443671398368, 1.036431515937792], | |
1908 [0.6965304744950663, 4.898419194187772, 0.9483351930487475, 1.036237452920916], | |
1909 [0.4683549692351834, 4.680698788736254, 0.942384914063441, 0.9233882406422014], | |
1910 [0.4806783117696812, 1.348428347467156, 0.9302636543778353, 0.7530765011973177], | |
1911 [0.7793672805674204, 4.787831141996395, 0.9480624914841251, 1.030500200806067] | |
1912 ] | |
1913 }, | |
1914 "M":{ | |
1915 "0": [ | |
1916 [11.12089148941739, 4.143408832044464, 0.9457653941884109, 0.9876159201486523], | |
1917 [1.056740916371472, 4.697466414277313, 0.9455811663390765, 0.9840807467893946], | |
1918 [1.45027528032305, 4.653773305076442, 0.9456320515081025, 0.9850547944267006], | |
1919 [1.632371493363489, 4.594239323176211, 0.9474694947403214, 1.021491622016719], | |
1920 [1.232114584038702, 3.928018554131193, 0.9455472732352994, 0.9834329726132869], | |
1921 [4.188756953953877, 4.367428082895338, 0.946432907777461, 1.000628598714736], | |
1922 [14.80469314176305, 8.266802561021329, 0.953467730194082, 1.160467313907541], | |
1923 [1.206142865652315, 4.740589478826124, 0.9479805115386509, 1.032082663580494], | |
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1928 [0.7379252351670703, 2.421050807990321, 0.9425853023190387, 0.9297768573626323], | |
1929 [0.8959277623945635, 3.018934262628716, 0.9437670236817639, 0.9505060355446658], | |
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1931 [0.6037992117999957, 4.365127533973584, 0.9473301554601188, 1.018639414637313], | |
1932 [0.6424292402420305, 3.699581154664379, 0.9452854995329421, 0.9784569184882379], | |
1933 [0.7294545326395003, 4.796164563121208, 0.9481590135916497, 1.035831401098195], | |
1934 [0.4897252793147067, 3.000689980404647, 0.9388361152601244, 0.8693124059827875], | |
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1936 [0.4016372609279709, 3.210246109200792, 0.936775099495381, 0.8391282352383457], | |
1937 [0.3891338210751467, 5.246947438335837, 0.9410514548067123, 0.9041103270398781], | |
1938 [2.175131581300846, 3.845213594110762, 0.9450472534483991, 0.9739693087586228], | |
1939 [0.92494235937555, 4.338831895779922, 0.9470614754492294, 1.013182054192166], | |
1940 [0.6596383147968479, 4.869891372620134, 0.9483574903395343, 1.040030056096358], | |
1941 [0.5896001616611386, 0.7306768375053631, 0.931577955900614, 0.7710886483247434], | |
1942 [0.8015130885981691, 4.164190231573866, 0.946843048120952, 1.008786068987851], | |
1943 [0.7736664292649782, 4.609038895864282, 0.9476088328906688, 1.024358977516337], | |
1944 [1.414904917402769, 4.875648471572473, 0.9476086564896694, 1.024355337824762], | |
1945 [0.8042007115138321, 2.768661107882043, 0.9436447725576627, 0.9483212503975447], | |
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1947 [0.7124239744648641, 3.609373979746267, 0.9456793810562887, 0.9859624181819162], | |
1948 [0.6103073219807762, 2.710828655162033, 0.9434899603241017, 0.9455681210976421], | |
1949 [1.025904160701012, 3.7838609111942, 0.9458432868413275, 0.989117847271004], | |
1950 [0.6048591264310915, 4.999536858980709, 0.9452102163668988, 0.9770346650178053], | |
1951 [1.291293311795129, 2.565198476526078, 0.9427489090449115, 0.9325957300087788], | |
1952 [0.6121329515755007, 2.011041760056481, 0.9402513897409885, 0.8912454523886248], | |
1953 [1.180219368618043, 4.889398981184226, 0.946016884890265, 0.9924807611859802], | |
1954 [1.105454513598039, 4.890626853490008, 0.9459951977362014, 0.9920594593096063], | |
1955 [1.605413857897039, 2.939206936718294, 0.9433222475272992, 0.9426025446770783], | |
1956 [1.293878631192419, 3.971462634670916, 0.9443578875537566, 0.9612008660695848], | |
1957 [0.9884548052730145, 2.95089925072461, 0.9437110951800234, 0.9495053434551489], | |
1958 [0.5986741279543244, 16.31252560522164, 0.9748423963984914, 2.194554091209314], | |
1959 [0.7883494484476586, 2.442313169511699, 0.9427973874647455, 0.9334340889015836], | |
1960 [0.3606858017902954, 5.283306272982982, 0.9398590567207423, 0.8850619010776035], | |
1961 [1.082484408515005, 3.518499698102375, 0.9440467322711303, 0.9555406988066132], | |
1962 [0.7189636065011923, 4.830475003829075, 0.9481083539609163, 1.034764872593254], | |
1963 [0.7089798693324995, 1.787550141705444, 0.9388855498380224, 0.8700613907948836], | |
1964 [0.8928681193634391, 7.719192553702568, 0.9562806678635116, 1.238776643030965], | |
1965 [1.91491856016437, 3.591378903133635, 0.9437515876984222, 0.9502296507712116], | |
1966 [1.518644327658945, 7.098739351534149, 0.9713807869639863, 1.922263735334442], | |
1967 [2.565627964363285, 4.347255542248531, 0.9532757087115202, 1.15546542537587], | |
1968 [0.9830387823664467, 5.359534534868056, 0.9493057774951067, 1.060544285747459], | |
1969 [0.7648264763794788, 3.171203875735396, 0.9443605547374315, 0.9612496579633081], | |
1970 [7.993395478079703, 4.040805907248204, 0.9457270305465383, 0.986877776465911], | |
1971 [5.525040253676158, 13.14856060469339, 0.9646678277605314, 1.546281667154188], | |
1972 [2.467014480149219, 6.15909859522141, 0.9542597645398716, 1.181542554066135], | |
1973 [1.862805646612138, 4.991667936230018, 0.9469444810973467, 1.010822968875406], | |
1974 [1.749151399183032, 4.056954912196582, 0.9467575638128177, 1.007075464672394], | |
1975 [1.027468687238526, 4.677210305710327, 0.9476939066320149, 1.026117169621167], | |
1976 [1.364512927085234, 6.728242479888183, 0.9607143695721333, 1.384974287872262], | |
1977 [0.9285869893975317, 0.8529698379842841, 0.92357913285826, 0.6844524804439922], | |
1978 [1.919503172586934, 2.100639572147981, 0.9406698052530856, 0.8979302050977519], | |
1979 [1.708524541398916, 3.343596525186294, 0.9499000915823059, 1.073796906709932], | |
1980 [0.351736659376683, 5.293336788811861, 0.9394016657262749, 0.8779540578781505], | |
1981 [0.460891201341427, 3.111047565190542, 0.9385055203589782, 0.864334506647766], | |
1982 [0.6667717946817246, 4.893763142017518, 0.9484067419256615, 1.041076946162406], | |
1983 [0.4897252793147067, 3.000689980404647, 0.9388361152601244, 0.8693124059827875], | |
1984 [0.5178176253295015, 1.88921095940703, 0.9393570794111731, 0.8772669230898767], | |
1985 [0.4022964728231313, 3.212013747796585, 0.9368052890174339, 0.8395561610686151], | |
1986 [0.321650341035935, 2.369009391488082, 0.9280744744836993, 0.7307703790540948], | |
1987 [1.00034417247337, 2.390886247295616, 0.942368674814798, 0.926069085034263], | |
1988 [3.576480160390781, 4.912463418562362, 0.9464010403673108, 0.9999999999999825], | |
1989 [0.6304491791341287, 10.60195246158876, 0.9721853938458079, 1.979508304542972], | |
1990 [0.9634894197943674, 3.701269164336891, 0.9607653949851229, 1.386849129846004], | |
1991 [0.6977249906525677, 9.224982864215468, 0.9566357269905871, 1.24938324430541], | |
1992 [3.939818549048507, 3.799963013305871, 0.9450905313546948, 0.9747815980889891], | |
1993 [0.5709587856636735, 4.596838702365027, 0.9478070980889466, 1.028465347930432], | |
1994 [1.039505678863528, 2.630181065498647, 0.9430472466455497, 0.9377776493900509], | |
1995 [0.9097093831078803, 2.177085547731798, 0.9417303648135809, 0.9153041380556556], | |
1996 [2.526679237746549, 5.604425938489465, 0.9490601002908647, 1.055156262511035], | |
1997 [0.6143822341889521, 4.99144829349619, 0.9452553661312254, 0.9778871671968672], | |
1998 [0.7109050460931223, 2.285113659581308, 0.9401538518211494, 0.8897005870522886], | |
1999 [0.3751626675457733, 5.259283661692849, 0.9404152463403344, 0.8938520988503982], | |
2000 [5.455700586348224, 3.627801977783612, 0.9430731452855284, 0.9382300531395277], | |
2001 [1.016259264608087, 3.035959574613738, 0.9440777559739074, 0.9561022181697556], | |
2002 [0.6143822341889521, 4.99144829349619, 0.9452553661312254, 0.9778871671968672], | |
2003 [1.032908633075195, 4.281093104759017, 0.9468420882152287, 1.008766830020827], | |
2004 [0.8199237165649182, 4.59487117092029, 0.9479767425824605, 1.032003788716895], | |
2005 [1.101718288847909, 4.418029065543203, 0.9465682873948348, 1.003307380063987], | |
2006 [0.460891201341427, 3.111047565190542, 0.9385055203589782, 0.864334506647766], | |
2007 [1.276187562389319, 3.408382441768387, 0.9535701245269068, 1.163151454840884], | |
2008 [0.8829765375508152, 4.193342038398979, 0.9467687445837998, 1.00729888787612], | |
2009 [1.432282172713598, 4.730843363181782, 0.9476999050738113, 1.026241353390664], | |
2010 [0.4897252793147067, 3.000689980404647, 0.9388361152601244, 0.8693124059827875], | |
2011 [0.7876822616008416, 2.341753235131878, 0.9424142223282147, 0.9268463551695403], | |
2012 [0.6789308236852126, 2.055976973212894, 0.9393904630979548, 0.8777813152884754], | |
2013 [5.035952976182944, 3.481205514313594, 0.9448849753518865, 0.9709348471556141], | |
2014 [0.685828931856048, 4.19008360097909, 0.9469306580559864, 1.010544926820485], | |
2015 [0.8773580655346431, 3.625328475412289, 0.9454657716851658, 0.9818785889769074], | |
2016 [0.7404773516223278, 2.354089803868313, 0.9423404166263065, 0.9255874751819483], | |
2017 [0.9860262100430436, 2.392371964339527, 0.9415454025965623, 0.9122287267924964], | |
2018 [0.6314365928467149, 3.545984507473279, 0.9449248429712103, 0.971678680604101], | |
2019 [0.9166469986789135, 3.382724153057069, 0.9446677288386036, 0.9669003866967235], | |
2020 [0.4390781996591052, 3.023386790938086, 0.9441892779758745, 0.958125887159292], | |
2021 [0.8174501673176641, 2.662801467671637, 0.9456733525769783, 0.9858467240555225], | |
2022 [0.5949286791473107, 4.855199985365434, 0.9483916052942347, 1.040754989747624], | |
2023 [0.2774120146479326, 5.383246375825815, 0.9346295047149334, 0.8097274503225026], | |
2024 [1.638938608699536, 6.622181056464417, 0.9517736985782244, 1.117714523222077], | |
2025 [0.3891338210751467, 5.246947438335837, 0.9410514548067123, 0.9041103270398781], | |
2026 [1.672573472501623, 1.565334460317754, 0.9417368229992319, 0.9154118726584828], | |
2027 [0.4016372609279709, 3.210246109200792, 0.936775099495381, 0.8391282352383457], | |
2028 [1.10611116994661, 3.204247768703003, 0.9445053002703785, 0.9639045815354055], | |
2029 [0.6048591264310915, 4.999536858980709, 0.9452102163668988, 0.9770346650178053], | |
2030 [1.183704342600694, 3.747025957429154, 0.9457922093994382, 0.9881324841951163], | |
2031 [0.9796980226888625, 4.89065560818871, 0.9459668952224912, 0.9915101539239576], | |
2032 [2.650957215935254, 2.983447339818136, 0.9432093403624113, 0.9406159323773107], | |
2033 [0.5609084500251574, 5.022151804998466, 0.9486407491224464, 1.046078428396997], | |
2034 [1.094502737260034, 3.607917562747081, 0.9457655872763142, 0.9876196379380793], | |
2035 [0.3000065933906724, 5.356426420563507, 0.936281938583415, 0.8321952689371248], | |
2036 [0.7005007469051636, 2.864662754206939, 0.9438721642857091, 0.952392646063643], | |
2037 [0.6676721537624958, 4.854491177020392, 0.9482918367089511, 1.038637625854309], | |
2038 [0.9796980226888625, 4.89065560818871, 0.9459668952224912, 0.9915101539239576], | |
2039 [0.7523669393973026, 3.696972087992259, 0.9447611318424926, 0.968631074474544], | |
2040 [0.3751626675457733, 5.259283661692849, 0.9404152463403344, 0.8938520988503982], | |
2041 [2.578355803805064, 1.194263087887754, 0.9358261860716989, 0.8258829371672378], | |
2042 [1.758575626961126, 3.479653608348491, 0.9439598778397863, 0.9539719673543295], | |
2043 [0.460891201341427, 3.111047565190542, 0.9385055203589782, 0.864334506647766], | |
2044 [0.4953459056315128, 5.121692978964261, 0.9488347404447115, 1.050259326587479], | |
2045 [0.5894218527649459, 4.976751327281332, 0.9485422551688979, 1.043967753758321], | |
2046 [1.014626712459672, 4.590005220246177, 0.9475074907258697, 1.022272008885547], | |
2047 [0.471291117065872, 3.719808931253234, 0.9448190962983778, 0.9697080586807237], | |
2048 [0.4897252793147067, 3.000689980404647, 0.9388361152601244, 0.8693124059827875], | |
2049 [0.7591559603606866, 1.656114653018429, 0.9380157365973468, 0.8570572455368082], | |
2050 [0.4897252793147067, 3.000689980404647, 0.9388361152601244, 0.8693124059827875], | |
2051 [0.9695853293652987, 4.690857359257484, 0.9477491291230797, 1.027261499734253], | |
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2053 [0.7769983305259213, 4.301127410735666, 0.9470588660370567, 1.013129324071796], | |
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2057 [3.080044657910243, 2.051589617170126, 0.939695162566787, 0.8825025950049379], | |
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2059 [2.418417455208109, 3.924188697111596, 0.9452688929133464, 0.9781428490216675], | |
2060 [5.039928724679458, 4.469627736498372, 0.9470705976642327, 1.013366433691771], | |
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2065 [0.7296783520450687, 2.145908633443113, 0.9489778711446172, 1.053364459461665], | |
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2069 [1.336999058600456, 4.543018278529006, 0.9472512467358681, 1.017030874370483], | |
2070 [1.697946232145576, 4.313609153680856, 0.9467795668440793, 1.007515236437644], | |
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2102 [0.7773082709004604, 4.719627465347147, 0.9479568036581688, 1.031586706789682] | |
2103 ] | |
2104 }, | |
2105 "N":{ | |
2106 "0": [ | |
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3059 }, | |
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3250 }, | |
3251 "V":{ | |
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3441 }, | |
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3802 [0.3520804297563899, 5.424243409593884, 0.9396383797375203, 0.8706542811180502], | |
3803 [2.544837494173256, 3.521920000609445, 0.9441990253231469, 0.9463845557170421], | |
3804 [0.603891841286635, 5.247388121876861, 0.9490427891677147, 1.041660093547123], | |
3805 [0.484008547844867, 5.312471991595352, 0.9491741113319426, 1.04449600902757], | |
3806 [1.373062847721786, 4.919405364816462, 0.9480354383653545, 1.02038293148906], | |
3807 [0.608233509184904, 5.237821884668473, 0.9490799424363097, 1.042460938373021], | |
3808 [0.669408147638378, 5.18380304298671, 0.94893521281611, 1.039347839662472], | |
3809 [1.1314690270324, 4.918935784351252, 0.9481680430690288, 1.023136525679374], | |
3810 [1.039856566432454, 4.983481224771734, 0.9483092515410069, 1.026084313419155], | |
3811 [0.7858251954421919, 5.119211756891519, 0.9487494157681934, 1.035377164640513], | |
3812 [3.194238175062835, 4.857690727275035, 0.9476012905863258, 1.011465175052791], | |
3813 [0.8755801126544244, 5.070276452246964, 0.9485704163897833, 1.031578896894695], | |
3814 [1.3153230993828, 4.881809164796187, 0.9479426671633739, 1.018464837502886], | |
3815 [0.9922396556240248, 5.196272068305198, 0.9465894291244804, 0.9912434069105044], | |
3816 [0.9404773317391132, 5.018308696019317, 0.9484141431498254, 1.028284417156412], | |
3817 [0.6341963490047597, 5.215265451237025, 0.9490203473875555, 1.041176922764438], | |
3818 [0.6972925318517915, 5.171176742053586, 0.9488914514568129, 1.038410015082761], | |
3819 [0.4727948404541072, 5.340150191153969, 0.9438033585435205, 0.9393275036179892], | |
3820 [0.5026959673044284, 5.318601143720054, 0.944382387250396, 0.9496890189012613], | |
3821 [0.780269492334137, 5.063524190169711, 0.9486043868001306, 1.032297696142919] | |
3822 ] | |
3823 } | |
3824 }, | |
3825 "headers": [ | |
3826 ["rate", "Mean posterior relative rate at a site"], | |
3827 ["bias", "Mean posterior bias parameter at a site"], | |
3828 ["Prob[bias>0]", "Posterior probability of substitution bias"], | |
3829 ["BayesFactor[bias>0]", "Empiricial Bayes Factor for substitution bias"] | |
3830 ] | |
3831 }, | |
3832 "analysis":{ | |
3833 "authors":"Sergei L Kosakovsky Pond", | |
3834 "citation":"TBD", | |
3835 "contact":"spond@temple.edu", | |
3836 "info":"FADE (FUBAR Approach to Directional Evolution) is a fast method to test whether or not a subset of sites in a protein alignment\n evolve towards a particular residue along a subset of branches at accelerated rates compared to reference model.\n FADE uses a random effects model and latent Dirichlet allocation (LDA) - inspired approximation methods to allocate sites to rate classes.", | |
3837 "requirements":"A protein alignment and a **rooted** phylogenetic tree (optionally annotated with {})", | |
3838 "version":"0.2" | |
3839 }, | |
3840 "branch attributes":{ | |
3841 "0":{ | |
3842 "Baboon":{ | |
3843 "GTR":0, | |
3844 "original name":"Baboon" | |
3845 }, | |
3846 "Cat":{ | |
3847 "GTR":0.5479738108231806, | |
3848 "original name":"Cat" | |
3849 }, | |
3850 "Chimp":{ | |
3851 "GTR":0.005354406956230157, | |
3852 "original name":"Chimp" | |
3853 }, | |
3854 "Cow":{ | |
3855 "GTR":0.5217716656054335, | |
3856 "original name":"Cow" | |
3857 }, | |
3858 "Horse":{ | |
3859 "GTR":0.3639593662085931, | |
3860 "original name":"Horse" | |
3861 }, | |
3862 "Human":{ | |
3863 "GTR":0, | |
3864 "original name":"Human" | |
3865 }, | |
3866 "Mouse":{ | |
3867 "GTR":0.1538063185305938, | |
3868 "original name":"Mouse" | |
3869 }, | |
3870 "Node1":{ | |
3871 "GTR":0.03774939091948738 | |
3872 }, | |
3873 "Node10":{ | |
3874 "GTR":0.04065491268006209 | |
3875 }, | |
3876 "Node13":{ | |
3877 "GTR":0.02528485699542644 | |
3878 }, | |
3879 "Node2":{ | |
3880 "GTR":0.4507260725563764 | |
3881 }, | |
3882 "Node3":{ | |
3883 "GTR":0.06938193079176812 | |
3884 }, | |
3885 "Node4":{ | |
3886 "GTR":0.2509978904573531 | |
3887 }, | |
3888 "Node9":{ | |
3889 "GTR":0.2259272621401927 | |
3890 }, | |
3891 "Pig":{ | |
3892 "GTR":0.3705420381298933, | |
3893 "original name":"Pig" | |
3894 }, | |
3895 "Rat":{ | |
3896 "GTR":0.1225892423633173, | |
3897 "original name":"Rat" | |
3898 }, | |
3899 "RhMonkey":{ | |
3900 "GTR":0.01051890950002691, | |
3901 "original name":"RhMonkey" | |
3902 } | |
3903 }, | |
3904 "attributes":{ | |
3905 "GTR":{ | |
3906 "attribute type":"branch length", | |
3907 "display order":0 | |
3908 }, | |
3909 "original name":{ | |
3910 "attribute type":"node label", | |
3911 "display order":-1 | |
3912 } | |
3913 } | |
3914 }, | |
3915 "data partitions":{ | |
3916 "0":{ | |
3917 "coverage": [ | |
3918 [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186] | |
3919 ], | |
3920 "name":"fade.filter.default" | |
3921 } | |
3922 }, | |
3923 "fits":{ | |
3924 "GTR":{ | |
3925 "AIC-c":5159.231849035938, | |
3926 "Equilibrium frequencies": [ | |
3927 [0.03384696455734124], | |
3928 [0.02379421855942317], | |
3929 [0.07116510014564366], | |
3930 [0.06063513939424073], | |
3931 [0.02621530635466421], | |
3932 [0.05270341130752417], | |
3933 [0.01804981525062285], | |
3934 [0.07446640012659383], | |
3935 [0.1050645690919535], | |
3936 [0.09185268026948845], | |
3937 [0.02464425428149188], | |
3938 [0.07033121952127283], | |
3939 [0.03713290409005404], | |
3940 [0.02697358951223052], | |
3941 [0.03378412161537671], | |
3942 [0.06364460641047323], | |
3943 [0.06994370764087279], | |
3944 [0.07542893941378664], | |
3945 [0.01961100044001494], | |
3946 [0.02071205201693066] | |
3947 ], | |
3948 "Log Likelihood":-2323.685267583662, | |
3949 "Rate Distributions":null, | |
3950 "display order":0, | |
3951 "estimated parameters":225 | |
3952 } | |
3953 }, | |
3954 "input":{ | |
3955 "file name":"/Users/ryanvelazquez/Documents/galaxy_items/tools-iuc/tools/hyphy/./test-data/fade-in1.fa", | |
3956 "number of sequences":10, | |
3957 "number of sites":187, | |
3958 "partition count":1, | |
3959 "trees":{ | |
3960 "0":"(((((Pig:0.147969,Cow:0.21343)Node4:0.08509899999999999,Horse:0.165787,Cat:0.264806)Node3:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node10:0.022733,(Human:0.004349,Chimp:0.000799)Node13:0.011873)Node9:0.101856)Node2:0.340802,Rat:0.050958)Node1:0.1,Mouse:0.09795)" | |
3961 } | |
3962 }, | |
3963 "settings":{ | |
3964 "bayes factor":100, | |
3965 "burn-in":1000000, | |
3966 "chain-length":2000000, | |
3967 "chains":1, | |
3968 "concentration":0.5, | |
3969 "grid size":20, | |
3970 "method":"Variational-Bayes", | |
3971 "samples":100 | |
3972 }, | |
3973 "site annotations":{ | |
3974 "headers":{ | |
3975 "Composition":"Amino acid composition of site", | |
3976 "Substitutions":"Substitution history on selected branches" | |
3977 }, | |
3978 "site annotations":{ | |
3979 "0": [ | |
3980 ["E1,K8", "K->E(1)"], | |
3981 ["E9", ""], | |
3982 ["I9", ""], | |
3983 ["A1,R6,T6", "R->T(1), T->A(1)R(1)"], | |
3984 ["D3,E1,K1,N11", "D->N(1), N->E(1)K(1)"], | |
3985 ["A7,D1,N5,S3,T1", "N->A(1)D(1)S(2), S->T(1)"], | |
3986 ["D1,E3,G1,I5,L7", "E->G(1)I(1), I->D(1)E(1)L(1)"], | |
3987 ["E7,I1,T6,V3", "T->E(1)I(1)V(1)"], | |
3988 ["I2,T7,V8", "V->I(2)T(1)"], | |
3989 ["L1,W16", "W->L(1)"], | |
3990 ["G17", ""], | |
3991 ["A14,I1,T1,V1", "A->I(1)T(1)V(1)"], | |
3992 ["L16,V1", "L->V(1)"], | |
3993 ["D3,E1,G13", "G->D(1)E(1)"], | |
3994 ["H4,Q12,R1", "H->Q(1), Q->H(1)R(1)"], | |
3995 ["D14,G3", "G->D(1)"], | |
3996 ["I16,L1", "I->L(1)"], | |
3997 ["D3,N13,T1", "N->D(1)T(1)"], | |
3998 ["L17", ""], | |
3999 ["D14,N3", "N->D(1)"], | |
4000 ["I17", ""], | |
4001 ["P17", ""], | |
4002 ["A1,D4,E1,G1,N3,S7", "D->A(1)E(1)G(1)S(1), N->D(1)"], | |
4003 ["F15,L1,S1", "F->L(1)S(1)"], | |
4004 ["P2,Q14,S1", "P->S(1), Q->P(1)"], | |
4005 ["K2,M13,R1", "K->R(1), M->K(1)"], | |
4006 ["G1,H1,S12,T3", "S->G(1)H(1), T->S(1)"], | |
4007 ["D15,E1,I1", "D->E(1)I(1)"], | |
4008 ["D13,H1,I1,N2", "D->H(1)I(1)N(2)"], | |
4009 ["I13,V4", "I->V(2)"], | |
4010 ["A1,D15,E1", "D->A(1)E(1)"], | |
4011 ["D13,E3,H1", "D->H(1), E->D(1)"], | |
4012 ["I14,V3", "V->I(1)"], | |
4013 ["H1,K7,Q1,R8", "K->R(1), R->H(1)K(2)Q(1)"], | |
4014 ["W17", ""], | |
4015 ["E13,N1,Q1,S1,V1", "E->N(1)Q(1)S(1)V(1)"], | |
4016 ["K13,R4", "K->R(1), R->K(1)"], | |
4017 ["T9", ""], | |
4018 ["S9", ""], | |
4019 ["D7,G6,N3,R1", "G->D(1)N(1)R(1)"], | |
4020 ["E1,G1,K13,S2", "K->E(1), S->G(1)K(1)"], | |
4021 ["K10,N3,T4", "K->N(1)T(1), T->K(1)"], | |
4022 ["K14,L3", "L->K(1)"], | |
4023 ["I13,V4", "I->V(1), V->I(1)"], | |
4024 ["A17", ""], | |
4025 ["E4,K4,Q7,R2", "E->K(1), K->E(1)Q(1)R(2)"], | |
4026 ["F16,I1", "F->I(1)"], | |
4027 ["K9,Q1,R7", "K->Q(1)R(1)"], | |
4028 ["I1,K12,N1,R3", "K->I(1)N(1), R->K(1)"], | |
4029 ["D2,E9,G1,K3,N1,S1", "D->N(1), E->D(1)G(1)S(1), K->E(1)"], | |
4030 ["K13,M2,N1,S1", "K->M(2)N(1)S(1)"], | |
4031 ["E8,K6,M1,P2", "K->E(2)M(1)P(2)"], | |
4032 ["L1,P4,T12", "P->T(1), T->L(1)P(1)"], | |
4033 ["F13,H3,K1", "F->H(1)K(1)"], | |
4034 ["E3,K4,L3,N2,P1,Q4", "K->E(1), L->Q(1), Q->K(1)N(2)P(1)"], | |
4035 ["E11,I1,K3,P1,V1", "E->K(1)P(1)V(1), K->E(1)I(1)"], | |
4036 ["D2,E2,K9,M1,S3", "E->D(2)K(2), K->M(1), S->E(1)"], | |
4037 ["D10,E5,G1,K1", "E->D(2)G(1)K(1)"], | |
4038 ["A4,K2,T11", "T->A(2)K(2)"], | |
4039 ["F1,Y16", "Y->F(1)"], | |
4040 ["D1,E7,K7,M1,N1", "E->D(1)K(1)M(1)N(1)"], | |
4041 ["I1,L7,M3,V6", "V->I(1)L(1)M(1)"], | |
4042 ["F8,L8,S1", "L->F(2)S(1)"], | |
4043 ["A3,K10,M1,P2,T1", "A->K(1), K->M(1)P(1), P->T(1)"], | |
4044 ["N17", ""], | |
4045 ["G17", ""], | |
4046 ["D1,S2,T14", "S->D(1)T(1)"], | |
4047 ["L17", ""], | |
4048 ["K16,R1", "K->R(1)"], | |
4049 ["I16", ""], | |
4050 ["K17", ""], | |
4051 ["D1,H12,K1,N2,T1", "H->D(1)T(1), N->H(1)K(1)"], | |
4052 ["P1", ""], | |
4053 ["L16,M1", "L->M(1)"], | |
4054 ["E1,K8,M7,T1", "M->E(1)K(2)T(1)"], | |
4055 ["I3,L1,R9,T4", "R->L(1)T(1), T->I(1)"], | |
4056 ["D10,E1,H3,I1,N2", "D->E(1)H(1)I(1)N(2)"], | |
4057 ["D16,H1", "D->H(1)"], | |
4058 ["C1,E5,Q7,S4", "E->C(1)Q(1)S(1), S->E(1)"], | |
4059 ["D8,G9", "G->D(2)"], | |
4060 ["I5,L1,S4,T7", "I->L(1), S->I(1), T->I(1)S(1)"], | |
4061 ["Y17", ""], | |
4062 ["E1,K13,N3", "K->E(1), N->K(1)"], | |
4063 ["V17", ""], | |
4064 ["D1,E1,M1,S10,T3,V1", "S->D(1)E(1)T(1)V(1), T->M(1)S(1)"], | |
4065 ["A1,I10,V6", "I->A(1)V(1), V->I(1)"], | |
4066 ["Y17", ""], | |
4067 ["A1,D13,G2,S1", "D->A(1), G->D(1)S(1)"], | |
4068 ["K1,S2,T14", "T->K(1)S(2)"], | |
4069 ["D5,K7,N5", "D->N(1), N->D(1)K(1)"], | |
4070 ["G17", ""], | |
4071 ["K13,M2,T1,V1", "K->V(1), M->K(1)T(1)"], | |
4072 ["H1,N13,R2,T1", "N->H(1), R->N(1)T(1)"], | |
4073 ["I2,L1,M1,R1,V12", "I->R(1)V(1), V->L(1)M(1)"], | |
4074 ["L17", ""], | |
4075 ["D2,E14,S1", "E->D(2)S(1)"], | |
4076 ["E1,K15,R1", "K->E(1)R(1)"], | |
4077 ["A2,D1,I3,K3,T8", "A->D(1)T(1), T->I(1)K(1)"], | |
4078 ["F14,L3", "L->F(1)"], | |
4079 ["D15,H1,Q1", "D->H(1)Q(1)"], | |
4080 ["L16,V1", "L->V(1)"], | |
4081 ["K12,P1,R3,S1", "K->P(1)S(1), R->K(1)"], | |
4082 ["I16,L1", "I->L(1)"], | |
4083 ["L5,Q12", "L->Q(1), Q->L(2)"], | |
4084 ["D1,E16", "E->D(1)"], | |
4085 ["G1,K1,M7,R8", "M->G(1)K(1)R(2)"], | |
4086 ["L1,V16", "V->L(1)"], | |
4087 ["S17", ""], | |
4088 ["E3,G1,K12,T1", "K->E(1)G(1)T(1)"], | |
4089 ["P17", ""], | |
4090 ["E2,K9,M3,N2,V1", "E->V(1), K->E(1)N(2), M->K(1)"], | |
4091 ["I17", ""], | |
4092 ["D1,H2,N1,S12,Y1", "H->S(1)Y(1), S->D(1)N(1)"], | |
4093 ["W17", ""], | |
4094 ["E3,I1,N1,S5,T7", "E->S(1), S->I(1)N(1)T(1)"], | |
4095 ["C17", ""], | |
4096 ["A2,I10,P1,S2,T2", "A->T(1), I->A(1)T(1), S->I(1)P(1)"], | |
4097 ["D1,N16", "N->D(1)"], | |
4098 ["A1,K3,R1,T12", "K->R(1), T->A(1)K(2)"], | |
4099 ["T17", ""], | |
4100 ["L14,V3", "L->V(1)"], | |
4101 ["S1,T15,V1", "T->S(1)V(1)"], | |
4102 ["C17", ""], | |
4103 ["A1,E14,K2", "E->A(1)K(2)"], | |
4104 ["V17", ""], | |
4105 ["A1,E1,L3,M7,S1,T4", "L->T(1), T->A(1)E(1)M(1)S(1)"], | |
4106 ["E3,K1,N12,Q1", "E->N(1)Q(1), N->E(1)K(1)"], | |
4107 ["G17", ""], | |
4108 ["S3,T14", "T->S(1)"], | |
4109 ["D15,N1", "D->N(1)"], | |
4110 ["F3,P13,V1", "F->P(1)V(1), P->F(1)"], | |
4111 ["E14,K3", "E->K(1)"], | |
4112 ["L17", ""], | |
4113 ["K9,N7,Q1", "K->N(1)Q(1)"], | |
4114 ["L17", ""], | |
4115 ["F1,Y16", "Y->F(1)"], | |
4116 ["L4,Q11,V2", "L->V(2), Q->L(1)"], | |
4117 ["D8,G3,N6", "D->N(1), G->D(1)"], | |
4118 ["E2,G11,K3,T1", "E->G(1)K(1), G->K(1), K->T(1)"], | |
4119 ["E1,K7,R1,S1,T7", "T->E(1)K(1)R(1)S(1)"], | |
4120 ["H11,L1,M1,R2,S1,T1", "H->L(1)M(1)R(1)S(1), R->T(1)"], | |
4121 ["A1,I4,L10,V2", "I->A(1)V(1), L->I(1)V(1)"], | |
4122 ["K12,N1,Q1,R3", "K->Q(1)R(1), R->K(1)N(1)"], | |
4123 ["E4,K1,P1,Q1,S3", "E->K(1)P(1)Q(1), S->E(1)"], | |
4124 ["D1,G2,L12,S1,V1", "G->D(1), L->G(1)S(1)V(1)"], | |
4125 ["H1,P3,R2,S11", "P->R(1)S(1), S->H(1)P(1)R(1)"], | |
4126 ["G1,Q14,R1,S1", "Q->G(1)R(1)S(1)"], | |
4127 ["K10,R7", "K->R(1)"], | |
4128 ["F1,L1,N1,T2,V12", "T->N(1)V(1), V->F(1)L(1)"], | |
4129 ["I13,M3,S1", "I->S(1), M->I(1)"], | |
4130 ["L1,S3,T12,V1", "S->T(1), T->L(1)V(1)"], | |
4131 ["H7,W1,Y9", "Y->H(1)W(1)"], | |
4132 ["K12,Q3,R1,T1", "K->R(1)T(1), Q->K(1)"], | |
4133 ["F1,R1,W15", "W->F(1)R(1)"], | |
4134 ["A4,I1,N3,T7", "A->I(1)N(1)T(1)"], | |
4135 ["N1,S1,T15", "T->N(1)S(1)"], | |
4136 ["K3,N6,R1,S7", "K->R(1), N->K(2)S(1)"], | |
4137 ["L11,Q3,W3", "L->Q(1), Q->W(1)"], | |
4138 ["I1,K1,N2,R2,S11", "R->N(1)S(1), S->I(1)K(1)N(1)"], | |
4139 ["A13,I1,K1,T2", "A->I(1)T(1), T->K(1)"], | |
4140 ["K7,L2,P3,S1,T4", "P->T(1), T->K(1)L(2)S(1)"], | |
4141 ["F16,V1", "F->V(1)"], | |
4142 ["K16,N1", "K->N(1)"], | |
4143 ["C17", ""], | |
4144 ["E1,K2,T11,V3", "K->E(1)T(1), T->V(1)"], | |
4145 ["A17", ""], | |
4146 ["E1,G7,I2,N1,S5,V1", "I->S(1)V(1), S->E(1)G(1)N(1)"], | |
4147 ["N17", ""], | |
4148 ["H1,K10,N2,P1,R2,T1", "K->N(1)T(1), N->H(1), R->K(1)P(1)"], | |
4149 ["A1,V16", "V->A(1)"], | |
4150 ["D1,S16", "S->D(1)"], | |
4151 ["E3,K12,Q1,S1", "E->S(1), K->E(2)Q(1)"], | |
4152 ["E15,K1,Q1", "E->K(1)Q(1)"], | |
4153 ["I2,S14,V1", "I->V(1), S->I(1)"], | |
4154 ["D1,E2,K1,R3,S10", "E->K(1)S(1), S->D(1)R(1)"], | |
4155 ["I1,M11,S1,V4", "M->I(1)S(1)V(2)"], | |
4156 ["E14,K1,V2", "E->K(1)V(2)"], | |
4157 ["I1,M1,P3,T5,V7", "T->P(1), V->I(1)M(1)T(2)"], | |
4158 ["A1,I5,V11", "I->A(1), V->I(1)"], | |
4159 ["N3,R1,S11,T1,V1", "N->S(1), S->R(1)T(1)V(1)"], | |
4160 ["C17", ""], | |
4161 ["P14,S1,T2", "P->S(1)T(2)"], | |
4162 ["D1,E15,G1", "E->D(1)G(1)"], | |
4163 ["E1,K15,Q1", "K->E(1)Q(1)"], | |
4164 ["G17", ""], | |
4165 ["L17", ""], | |
4166 ["D14,P1,S2", "S->D(1)P(1)"] | |
4167 ] | |
4168 } | |
4169 }, | |
4170 "tested":{ | |
4171 "0":{ | |
4172 "Baboon":"test", | |
4173 "Cat":"test", | |
4174 "Chimp":"test", | |
4175 "Cow":"test", | |
4176 "Horse":"test", | |
4177 "Human":"test", | |
4178 "Mouse":"test", | |
4179 "Node1":"test", | |
4180 "Node10":"test", | |
4181 "Node13":"test", | |
4182 "Node2":"test", | |
4183 "Node3":"test", | |
4184 "Node4":"test", | |
4185 "Node9":"test", | |
4186 "Pig":"test", | |
4187 "Rat":"test", | |
4188 "RhMonkey":"test" | |
4189 } | |
4190 }, | |
4191 "timers":{ | |
4192 "Baseline Fit":{ | |
4193 "order":1, | |
4194 "timer":88 | |
4195 }, | |
4196 "Overall":{ | |
4197 "order":0, | |
4198 "timer":121 | |
4199 }, | |
4200 "Residue A analysis":{ | |
4201 "order":2, | |
4202 "timer":2 | |
4203 }, | |
4204 "Residue C analysis":{ | |
4205 "order":3, | |
4206 "timer":1 | |
4207 }, | |
4208 "Residue D analysis":{ | |
4209 "order":4, | |
4210 "timer":1 | |
4211 }, | |
4212 "Residue E analysis":{ | |
4213 "order":5, | |
4214 "timer":1 | |
4215 }, | |
4216 "Residue F analysis":{ | |
4217 "order":6, | |
4218 "timer":2 | |
4219 }, | |
4220 "Residue G analysis":{ | |
4221 "order":7, | |
4222 "timer":1 | |
4223 }, | |
4224 "Residue H analysis":{ | |
4225 "order":8, | |
4226 "timer":2 | |
4227 }, | |
4228 "Residue I analysis":{ | |
4229 "order":9, | |
4230 "timer":1 | |
4231 }, | |
4232 "Residue K analysis":{ | |
4233 "order":10, | |
4234 "timer":2 | |
4235 }, | |
4236 "Residue L analysis":{ | |
4237 "order":11, | |
4238 "timer":1 | |
4239 }, | |
4240 "Residue M analysis":{ | |
4241 "order":12, | |
4242 "timer":2 | |
4243 }, | |
4244 "Residue N analysis":{ | |
4245 "order":13, | |
4246 "timer":2 | |
4247 }, | |
4248 "Residue P analysis":{ | |
4249 "order":14, | |
4250 "timer":1 | |
4251 }, | |
4252 "Residue Q analysis":{ | |
4253 "order":15, | |
4254 "timer":2 | |
4255 }, | |
4256 "Residue R analysis":{ | |
4257 "order":16, | |
4258 "timer":2 | |
4259 }, | |
4260 "Residue S analysis":{ | |
4261 "order":17, | |
4262 "timer":2 | |
4263 }, | |
4264 "Residue T analysis":{ | |
4265 "order":18, | |
4266 "timer":2 | |
4267 }, | |
4268 "Residue V analysis":{ | |
4269 "order":19, | |
4270 "timer":2 | |
4271 }, | |
4272 "Residue W analysis":{ | |
4273 "order":20, | |
4274 "timer":2 | |
4275 }, | |
4276 "Residue Y analysis":{ | |
4277 "order":21, | |
4278 "timer":2 | |
4279 } | |
4280 } | |
4281 } |