{
"MLE":{
"content":{
"0":{
"by-branch":{
"AVERAGED": [
[0, 0, 0, 0, null, null, null, 0, 1, 1, 0],
[0, 0, 0, 0, null, null, null, 0, 1, 1, 0],
[64.53821744330372, 156.0433563061894, 4, 16, 0.2925820880967943, 0.06197878030198101, 0.102535605351917, 0, 0.2602823906814491, 0.8793871013571201, 0.1296907440255211]
],
"NAMES": [
["epi_isl_444721_New_York_20200403_null_6"],
["epi_isl_468296_Bern_20200501_null_1"],
["epi_isl_430719_Madrid_20200311_null_1"]
],
"RESOLVED": [
[0, 0, 0, 0, null, null, null, 0, 1, 1, 0],
[0, 0, 0, 0, null, null, null, 0, 1, 1, 0],
[64.53821744330372, 156.0433563061894, 4, 16, 0.2925820880967943, 0.06197878030198101, 0.102535605351917, 0, 0.2602823906814491, 0.8793871013571201, 0.1296907440255211]
]
},
"by-site":{
"AVERAGED": [
[0, 3, 0, 0, 0, null, 0, null, 1, 1, 0.1296907440255211],
[0.5363607380531245, 2, 0, 0, 0.2114686329929659, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 1.536360738053125, 0, 0, 0.394265683503517, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.5363607380531245, 2.463639261946875, 0, 0, 0.1787869126843748, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 1.614106226458817, 0, 0, 0.3825399250720747, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.3176625293653235, 2.682337470634677, 0, 0, 0.1058875097884412, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.8321225793947096, 2.16787742060529, 0, 0, 0.2773741931315699, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.8659624551217401, 1.682337470634677, 0, 0, 0.3398196760001454, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.6823374706346764, 2.317662529365323, 0, 0, 0.2274458235448922, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.5482999257564166, 2.451700074243583, 0, 0, 0.1827666419188055, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.5363607380531245, 2.463639261946875, 0, 0, 0.1787869126843748, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.5482999257564166, 2.451700074243583, 0, 0, 0.1827666419188055, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.5363607380531245, 2.463639261946875, 0, 0, 0.1787869126843748, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.5363607380531245, 2.463639261946875, 0, 0, 0.1787869126843748, 0, 0, 0, 1, 1, 0.1296907440255211],
[1.380422505151126, 1.16787742060529, 0, 0, 0.5417033101946871, 0, 0, 0, 1, 1, 0.1296907440255211],
[1.536360738053125, 1.463639261946875, 0, 0, 0.5121202460177082, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1.536360738053125, 1.463639261946875, 0, 0, 0.5121202460177082, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.9222545115943069, 2.077745488405693, 0, 0, 0.3074181705314357, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1.192946886770591, 1.538872744202846, 1, 0, 0.4366858167519299, 0.8382602872681827, 0, -6.463532101436832, 1, 0.4366858167519299, 0.1296907440255211],
[1.380422505151126, 1.16787742060529, 0, 0, 0.5417033101946871, 0, 0, 0, 1, 1, 0],
[0.5482999257564166, 2, 0, 0, 0.2151630270105132, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[0.5363607380531245, 2, 0, 0, 0.2114686329929659, 0, 0, 0, 1, 1, 0],
[0.5363607380531245, 2.077745488405693, 0, 0, 0.2051793965464449, 0, 0, 0, 1, 1, 0],
[0.5363607380531245, 2.077745488405693, 0, 0, 0.2051793965464449, 0, 0, 0, 1, 1, 0],
[0.5482999257564166, 2.451700074243583, 0, 0, 0.1827666419188055, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[0.5363607380531245, 2.463639261946875, 0, 0, 0.1787869126843748, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[0.5482999257564166, 2.451700074243583, 0, 0, 0.1827666419188055, 0, 0, 0, 1, 1, 0],
[0.9247166542927361, 2.075283345707264, 0, 2, 0.3082388847642454, 0, 0.9637238231285439, 7.430937576693199, 0.4785334405522149, 1, 0.1296907440255211],
[0.6058875097884411, 2.272699969891286, 0, 2, 0.2104808396706611, 0, 0.8800105717850957, 6.785453953536757, 0.6233405045271443, 1, 0.1296907440255211],
[0.726756262369586, 1.822944588123442, 0.5, 1.5, 0.2850358943987705, 0.6879885676798324, 0.8228445394185655, 1.039827265638908, 0.7149641056012295, 0.488826327701834, 0.1296907440255211],
[1, 2, 0, 1, 0.3333333333333333, 0, 0.5, 3.855325248975423, 0.6666666666666667, 1, 0.1296907440255211],
[0.7447218684206589, 2.107010032827232, 0.5, 2.5, 0.2611472235853502, 0.6713915908772174, 1.18651547028727, 3.971940197279495, 0.6171840071360345, 0.5966577386251599, 0.1296907440255211],
[0.5482999257564166, 2.225850037121792, 0, 1, 0.1976461017224714, 0, 0.4492665648280074, 3.464137461803741, 0.8023538982775286, 1, 0.1296907440255211],
[0.5423303319047705, 2, 1, 0, 0.2133201673672534, 1.84389465455086, 0, -14.21762723628149, 1, 0.2133201673672533, 0.1296907440255211],
[1, 2, 0, 1, 0.3333333333333333, 0, 0.5, 3.855325248975423, 0.6666666666666667, 1, 0.1296907440255211],
[0.5423303319047705, 2.234318692439482, 1, 2, 0.195318287313194, 1.84389465455086, 0.8951274528417219, -7.315612296297995, 0.9004547857670886, 0.4789584047846871, 0.1296907440255211],
[0.7741499628782083, 2.225850037121792, 0, 1, 0.2580499876260694, 0, 0.4492665648280074, 3.464137461803741, 0.7419500123739307, 1, 0.1296907440255211],
[0.9247166542927361, 2, 0, 2, 0.3161730737011698, 0, 1, 7.710650497950845, 0.4676192651313057, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.3176625293653235, 2.318099909673857, 0, 0, 0.1205201670151736, 0, 0, 0, 1, 1, 0],
[0.5482999257564166, 2.451700074243583, 0, 0, 0.1827666419188055, 0, 0, 0, 1, 1, 0],
[1.536360738053125, 1.463639261946875, 0, 0, 0.5121202460177082, 0, 0, 0, 1, 1, 0],
[0.5482999257564166, 2.451700074243583, 0, 0, 0.1827666419188055, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[0.6357624390391808, 2, 0, 0, 0.2412062747471796, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[0.5482999257564166, 2.451700074243583, 0, 0, 0.1827666419188055, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[1.536360738053125, 1.463639261946875, 0, 0, 0.5121202460177082, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[0.3176625293653235, 2.318099909673857, 0, 0, 0.1205201670151736, 0, 0, 0, 1, 1, 0]
],
"RESOLVED": [
[0, 3, 0, 0, 0, null, 0, null, 1, 1, 0.1296907440255211],
[0.5363607380531245, 2, 0, 0, 0.2114686329929659, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 1.536360738053125, 0, 0, 0.394265683503517, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.5363607380531245, 2.463639261946875, 0, 0, 0.1787869126843748, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 1.614106226458817, 0, 0, 0.3825399250720747, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.3176625293653235, 2.682337470634677, 0, 0, 0.1058875097884412, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.8321225793947096, 2.16787742060529, 0, 0, 0.2773741931315699, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.8659624551217401, 1.682337470634677, 0, 0, 0.3398196760001454, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.6823374706346764, 2.317662529365323, 0, 0, 0.2274458235448922, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.5482999257564166, 2.451700074243583, 0, 0, 0.1827666419188055, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.5363607380531245, 2.463639261946875, 0, 0, 0.1787869126843748, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.5482999257564166, 2.451700074243583, 0, 0, 0.1827666419188055, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.5363607380531245, 2.463639261946875, 0, 0, 0.1787869126843748, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.5363607380531245, 2.463639261946875, 0, 0, 0.1787869126843748, 0, 0, 0, 1, 1, 0.1296907440255211],
[1.380422505151126, 1.16787742060529, 0, 0, 0.5417033101946871, 0, 0, 0, 1, 1, 0.1296907440255211],
[1.536360738053125, 1.463639261946875, 0, 0, 0.5121202460177082, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1.536360738053125, 1.463639261946875, 0, 0, 0.5121202460177082, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.9222545115943069, 2.077745488405693, 0, 0, 0.3074181705314357, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[1.192946886770591, 1.538872744202846, 1, 0, 0.4366858167519299, 0.8382602872681827, 0, -6.463532101436832, 1, 0.4366858167519299, 0.1296907440255211],
[1.380422505151126, 1.16787742060529, 0, 0, 0.5417033101946871, 0, 0, 0, 1, 1, 0],
[0.5482999257564166, 2, 0, 0, 0.2151630270105132, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[0.5363607380531245, 2, 0, 0, 0.2114686329929659, 0, 0, 0, 1, 1, 0],
[0.5363607380531245, 2.077745488405693, 0, 0, 0.2051793965464449, 0, 0, 0, 1, 1, 0],
[0.5363607380531245, 2.077745488405693, 0, 0, 0.2051793965464449, 0, 0, 0, 1, 1, 0],
[0.5482999257564166, 2.451700074243583, 0, 0, 0.1827666419188055, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[0.5363607380531245, 2.463639261946875, 0, 0, 0.1787869126843748, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[0.5482999257564166, 2.451700074243583, 0, 0, 0.1827666419188055, 0, 0, 0, 1, 1, 0],
[0.9247166542927361, 2.075283345707264, 0, 2, 0.3082388847642454, 0, 0.9637238231285439, 7.430937576693199, 0.4785334405522149, 1, 0.1296907440255211],
[0.6058875097884411, 2.272699969891286, 0, 2, 0.2104808396706611, 0, 0.8800105717850957, 6.785453953536757, 0.6233405045271443, 1, 0.1296907440255211],
[0.726756262369586, 1.822944588123442, 0.5, 1.5, 0.2850358943987705, 0.6879885676798324, 0.8228445394185655, 1.039827265638908, 0.7149641056012295, 0.488826327701834, 0.1296907440255211],
[1, 2, 0, 1, 0.3333333333333333, 0, 0.5, 3.855325248975423, 0.6666666666666667, 1, 0.1296907440255211],
[0.7447218684206589, 2.107010032827232, 0.5, 2.5, 0.2611472235853502, 0.6713915908772174, 1.18651547028727, 3.971940197279495, 0.6171840071360345, 0.5966577386251599, 0.1296907440255211],
[0.5482999257564166, 2.225850037121792, 0, 1, 0.1976461017224714, 0, 0.4492665648280074, 3.464137461803741, 0.8023538982775286, 1, 0.1296907440255211],
[0.5423303319047705, 2, 1, 0, 0.2133201673672534, 1.84389465455086, 0, -14.21762723628149, 1, 0.2133201673672533, 0.1296907440255211],
[1, 2, 0, 1, 0.3333333333333333, 0, 0.5, 3.855325248975423, 0.6666666666666667, 1, 0.1296907440255211],
[0.5423303319047705, 2.234318692439482, 1, 2, 0.195318287313194, 1.84389465455086, 0.8951274528417219, -7.315612296297995, 0.9004547857670886, 0.4789584047846871, 0.1296907440255211],
[0.7741499628782083, 2.225850037121792, 0, 1, 0.2580499876260694, 0, 0.4492665648280074, 3.464137461803741, 0.7419500123739307, 1, 0.1296907440255211],
[0.9247166542927361, 2, 0, 2, 0.3161730737011698, 0, 1, 7.710650497950845, 0.4676192651313057, 1, 0.1296907440255211],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0.1296907440255211],
[0.3176625293653235, 2.318099909673857, 0, 0, 0.1205201670151736, 0, 0, 0, 1, 1, 0],
[0.5482999257564166, 2.451700074243583, 0, 0, 0.1827666419188055, 0, 0, 0, 1, 1, 0],
[1.536360738053125, 1.463639261946875, 0, 0, 0.5121202460177082, 0, 0, 0, 1, 1, 0],
[0.5482999257564166, 2.451700074243583, 0, 0, 0.1827666419188055, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[0.6357624390391808, 2, 0, 0, 0.2412062747471796, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[0.5482999257564166, 2.451700074243583, 0, 0, 0.1827666419188055, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[1.536360738053125, 1.463639261946875, 0, 0, 0.5121202460177082, 0, 0, 0, 1, 1, 0],
[1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 0],
[0.3176625293653235, 2.318099909673857, 0, 0, 0.1205201670151736, 0, 0, 0, 1, 1, 0]
]
}
}
},
"headers": [
["ES", "Expected synonymous sites"],
["EN", "Expected non-synonymous sites"],
["S", "Inferred synonymous substitutions"],
["N", "Inferred non-synonymous substitutions"],
["P[S]", "Expected proportion of synonymous sites"],
["dS", "Inferred synonymous susbsitution rate"],
["dN", "Inferred non-synonymous susbsitution rate"],
["dN-dS", "Scaled by the length of the tested branches"],
["P [dN/dS > 1]", "Binomial probability that S is no greater than the observed value, with Ps probability of success"],
["P [dN/dS < 1]", "Binomial probability that S is no less than the observed value, with Ps probability of success"],
["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
]
},
"analysis":{
"authors":"Sergei L Kosakovsky Pond and Simon DW Frost",
"citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222",
"contact":"spond@temple.edu",
"info":"SLAC (Single Likelihood Ancestor Counting)\n uses a maximum likelihood ancestral state reconstruction\n and minimum path substitution counting to estimate site - level\n dS and dN,\n and applies a simple binomial - based test to test\n if dS differs drom dN.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ",
"requirements":"in-frame codon alignment and a phylogenetic tree",
"version":"2.00"
},
"branch attributes":{
"0":{
"Node3":{
"amino-acid": [
["M", "Y", "S", "F", "V", "S", "E", "E", "T", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "L", "C", "A", "Y", "C", "C", "N", "I", "V", "N", "V", "S", "L", "V", "K", "P", "S", "F", "Y", "V", "Y", "S", "R", "V", "K", "N", "L", "N", "S", "S", "R", "V", "P", "D", "L", "L", "V", "K"]
],
"codon": [
["ATG", "TAC", "TCA", "TTC", "GTT", "TCG", "GAA", "GAG", "ACA", "GGT", "ACG", "TTA", "ATA", "GTT", "AAT", "AGC", "GTA", "CTT", "CTT", "TTT", "CTT", "GCT", "TTC", "GTG", "GTA", "TTC", "TTG", "CTA", "GTT", "ACA", "CTA", "GCC", "ATC", "CTT", "ACT", "GCG", "CTT", "CGA", "TTG", "TGT", "GCG", "TAC", "TGC", "TGC", "AAT", "ATT", "GTT", "AAC", "GTG", "AGT", "CTT", "GTA", "AAA", "CCT", "TCT", "TTT", "TAC", "GTT", "TAC", "TCT", "CGT", "GTT", "AAA", "AAT", "CTG", "AAT", "TCT", "TCT", "AGA", "GTT", "CCT", "GAT", "CTT", "CTG", "GTC", "AAA"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_430719_Madrid_20200311_null_1":{
"Global MG94xREV":0.1296907440255211,
"Nucleotide GTR":0.1481954837452034,
"amino-acid": [
["M", "Y", "S", "F", "V", "S", "E", "E", "T", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "S", "K", "R", "T", "K", "Y", "Y", "I", "S", "F", "S", "V", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"]
],
"codon": [
["ATG", "TAC", "TCA", "TTC", "GTT", "TCG", "GAA", "GAG", "ACA", "GGT", "ACG", "TTA", "ATA", "GTT", "AAT", "AGC", "GTA", "CTT", "CTT", "TTT", "CTT", "GCT", "TTC", "GTG", "GTA", "TTC", "TTG", "CTA", "GTT", "ACA", "CTA", "GCC", "ATC", "CTT", "ACT", "GCG", "CTT", "CGC", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "TCT", "AAA", "CGA", "ACT", "AAA", "TAT", "TAT", "ATT", "AGT", "TTT", "TCT", "GTT", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---", "---"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 1.5, 1, 2.5, 1, 0, 1, 2, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
],
"original name":"epi_isl_430719_Madrid_20200311_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 0, 0.5, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_444721_New_York_20200403_null_6":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "Y", "S", "F", "V", "S", "E", "E", "T", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "L", "C", "A", "Y", "C", "C", "N", "I", "V", "N", "V", "S", "L", "V", "K", "P", "S", "F", "Y", "V", "Y", "S", "R", "V", "K", "N", "L", "N", "S", "S", "R", "V", "P", "D", "L", "L", "V", "Y"]
],
"codon": [
["ATG", "TAC", "TCA", "TTC", "GTT", "TCG", "GAA", "GAG", "ACA", "GGT", "ACG", "TTA", "ATA", "GTT", "AAT", "AGC", "GTA", "CTT", "CTT", "TTT", "CTT", "GCT", "TTC", "GTG", "GTA", "TTC", "TTG", "CTA", "GTT", "ACA", "CTA", "GCC", "ATC", "CTT", "ACT", "GCG", "CTT", "CGA", "TTG", "TGT", "GCG", "TAC", "TGC", "TGC", "AAT", "ATT", "GTT", "AAC", "GTG", "AGT", "CTT", "GTA", "AAA", "CCT", "TCT", "TTT", "TAC", "GTT", "TAC", "TCT", "CGT", "GTT", "AAA", "AAT", "CTG", "AAT", "TCT", "TCT", "AGA", "GTT", "CCT", "GAT", "CTT", "CTG", "GTC", "TAN"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4]
],
"original name":"epi_isl_444721_New_York_20200403_null_6",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
},
"epi_isl_468296_Bern_20200501_null_1":{
"Global MG94xREV":0,
"Nucleotide GTR":0,
"amino-acid": [
["M", "Y", "S", "F", "V", "S", "E", "E", "KTRI", "G", "T", "L", "I", "V", "N", "S", "V", "L", "L", "F", "L", "A", "F", "V", "V", "F", "L", "L", "V", "T", "L", "A", "I", "L", "T", "A", "L", "R", "L", "C", "A", "Y", "C", "C", "N", "I", "V", "N", "V", "S", "L", "V", "K", "P", "S", "F", "Y", "V", "Y", "S", "R", "V", "K", "N", "L", "N", "S", "S", "R", "V", "P", "D", "L", "L", "V", "KQE"]
],
"codon": [
["ATG", "TAC", "TCA", "TTC", "GTT", "TCG", "GAA", "GAG", "ANA", "GGT", "ACG", "TTA", "ATA", "GTT", "AAT", "AGC", "GTA", "CTT", "CTT", "TTT", "CTT", "GCT", "TTC", "GTG", "GTA", "TTC", "TTG", "CTA", "GTT", "ACA", "CTA", "GCC", "ATC", "CTT", "ACT", "GCG", "CTT", "CGA", "TTG", "TGT", "GCG", "TAC", "TGC", "TGC", "AAT", "ATT", "GTT", "AAC", "GTG", "AGT", "CTT", "GTA", "AAA", "CCT", "TCT", "TTT", "TAC", "GTT", "TAC", "TCT", "CGT", "GTT", "AAA", "AAT", "CTG", "AAT", "TCT", "TCT", "AGA", "GTT", "CCT", "GAT", "CTT", "CTG", "GTC", "NAA"]
],
"nonsynonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2]
],
"original name":"epi_isl_468296_Bern_20200501_null_1",
"synonymous substitution count": [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
]
}
},
"attributes":{
"Global MG94xREV":{
"attribute type":"branch length",
"display order":1
},
"Nucleotide GTR":{
"attribute type":"branch length",
"display order":0
},
"amino-acid":{
"attribute type":"node label",
"display order":1
},
"codon":{
"attribute type":"node label",
"display order":0
},
"nonsynonymous substitution count":{
"attribute type":"branch label",
"display order":1
},
"original name":{
"attribute type":"node label",
"display order":-1
},
"synonymous substitution count":{
"attribute type":"branch label",
"display order":0
}
}
},
"data partitions":{
"0":{
"coverage": [
[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]
],
"name":"slac.filter.default"
}
},
"fits":{
"Global MG94xREV":{
"AIC-c":inf,
"Equilibrium frequencies": [
[0.01219270998446214],
[0.008976505750486209],
[0.008265769417181792],
[0.02234838349818919],
[0.01211701146590341],
[0.008920775056652626],
[0.00821445133445645],
[0.02220963341513537],
[0.007022552129071923],
[0.005170136880975284],
[0.004760778915681575],
[0.01287184623570358],
[0.0272445542776335],
[0.02005796073672453],
[0.01846982367494953],
[0.04993735994784623],
[0.009521220397734041],
[0.00700970413967215],
[0.006454694032592395],
[0.01745173018061649],
[0.00946210783950063],
[0.006966184346321502],
[0.006414620023070331],
[0.01734338100125908],
[0.005483872466472003],
[0.00403733155245638],
[0.003717666161079379],
[0.01005155417393317],
[0.0212751231060155],
[0.01566315160016288],
[0.01442298407331782],
[0.03899581067296212],
[0.01340419962116654],
[0.009868427538537436],
[0.009087071162328294],
[0.02456895915689468],
[0.01332097956138649],
[0.009807159342531508],
[0.009030654022422351],
[0.02441642261554522],
[0.007720325564053071],
[0.005683850998642874],
[0.005233818488208035],
[0.01415081607421199],
[0.02995162228844042],
[0.02205095586224892],
[0.0203050186400126],
[0.05489922602505877],
[0.01149747614690275],
[0.02862472473527328],
[0.01551996446873837],
[0.01142609399210747],
[0.01052140564525244],
[0.02844700794717835],
[0.006622123030669902],
[0.006097800585797172],
[0.01648678775185833],
[0.03489594076438061],
[0.02569105747116701],
[0.02365690648933521],
[0.06396181552143053]
],
"Log Likelihood":-inf,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *test*": [
[0.9165418920175951, 1]
]
},
"display order":1,
"estimated parameters":18
},
"Nucleotide GTR":{
"AIC-c":777.8636032896545,
"Equilibrium frequencies": [
[0.2190594059405941],
[0.195957095709571],
[0.1811056105610561],
[0.4038778877887788]
],
"Log Likelihood":-377.7353730733987,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.9254830449410044,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.5141627005595938,
"Substitution rate from nucleotide C to nucleotide G":0.2255308167046667,
"Substitution rate from nucleotide C to nucleotide T":0.6977012556247028,
"Substitution rate from nucleotide G to nucleotide T":0
},
"display order":0,
"estimated parameters":11
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-06-18/sequences.E.compressed.fas",
"number of sequences":3,
"number of sites":76,
"partition count":1,
"trees":{
"0":"(epi_isl_444721_New_York_20200403_null_6:1e-10,epi_isl_468296_Bern_20200501_null_1:0.00054894,epi_isl_430719_Madrid_20200311_null_1:0.1479)"
}
},
"tested":{
"0":{
"epi_isl_430719_Madrid_20200311_null_1":"test",
"epi_isl_444721_New_York_20200403_null_6":"test",
"epi_isl_468296_Bern_20200501_null_1":"test"
}
},
"timers":{
"Model fitting":{
"order":1,
"timer":0
},
"Primary SLAC analysis":{
"order":2,
"timer":1
},
"Total time":{
"order":0,
"timer":1
}
}
}