Mercurial > repos > iuc > hyphy_sm19
diff test-data/summary/ORF6.MEME-full.json @ 26:af92956bfe88 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
| author | iuc |
|---|---|
| date | Wed, 09 Jun 2021 07:05:34 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/ORF6.MEME-full.json Wed Jun 09 07:05:34 2021 +0000 @@ -0,0 +1,2444 @@ +{ + "MLE":{ + "content":{ + "0": [ +[235.7472979068722, 0, 1, 0.9943760343206508, 0, 0, 0.6666666666666666, 0, 0, -31.93549672470295, -31.93549672470295], + [3.125033384621221, 0, 1, 6.6249901946859, 0, 0, 0.6666666666666666, 0, 0, -43.49839666606186, -43.49831167050982], + [1.901386439598346, 0, 1, 3.602316293041297, 0, 0, 0.6666666666666666, 0, 0, -17.09092958578331, -17.09092776449802], + [1.622684212345616, 0, 1, 3.145879239633445, 0, 0, 0.6666666666666666, 0, 0, -61.02813244305516, -61.02813244305516], + [0.8148105398437983, 0, 1, 1.499991884237639, 0, 0, 0.6666666666666666, 0, 0, -25.26062185068822, -25.26062185068822], + [0.538978592942964, 0.01746277867903197, 1e-08, 9.230771679231886, 0.9999999899999999, 3.131671475355084, 0.09963705217536034, 1, 0, -30.93250048026707, -30.93322087121525], + [1.853606022970019, 0, 1, 3.674707574937826, 0, 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proportion of the tree evolving neutrally or under positive selection"], + ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p<sup>+</sup> > 0 <emph>and<emph> β<sup>+</sup> > α"], + ["p-value", "Asymptotic p-value for episodic diversification, i.e., p<sup>+</sup> > 0 <emph>and<emph> β<sup>+</sup> > α"], + ["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the β<sup>+</sup> rate"], + ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"], + ["MEME LogL", "Site Log-likelihood under the MEME model"], + ["FEL LogL", "Site Log-likelihood under the FEL model"] + ] + }, + "analysis":{ + "authors":"Sergei L. Kosakovsky Pond, Steven Weaver", + "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.", + "contact":"spond@temple.edu", + "info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if β+ > α at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. 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":"2.1.2" + }, + "branch attributes":{ + "0":{ + "Node100":{ + "Global MG94xREV":0.005595771389995104, + "Nucleotide GTR":0.005480709230504446 + }, + "Node112":{ + "Global MG94xREV":0.005601039668885619, + "Nucleotide GTR":0.005479616709115599 + }, + "Node115":{ + "Global MG94xREV":0.005593919439547744, + "Nucleotide GTR":0.0054731375250642 + }, + "Node119":{ + "Global MG94xREV":0.00560632712449723, + "Nucleotide GTR":0.00547792745634657 + }, + "Node172":{ + "Global MG94xREV":0.005628805315829838, + "Nucleotide GTR":0.005503005696410831 + }, + "Node177":{ + "Global MG94xREV":0.005582953695602026, + "Nucleotide GTR":0.005475013711016215 + }, + "Node184":{ + "Global MG94xREV":0.005597986108256508, + "Nucleotide GTR":0.005474986566233221 + }, + "Node194":{ + "Global MG94xREV":0.005557725672243263, + "Nucleotide GTR":0.005498938135253649 + }, + "Node198":{ + "Global MG94xREV":0.005634884025943302, + "Nucleotide GTR":0.005501809093221373 + }, + "Node201":{ + "Global MG94xREV":0.005588355805518057, + "Nucleotide GTR":0.005472956903151315 + }, + "Node206":{ + "Global MG94xREV":0.005633043010542594, + "Nucleotide GTR":0.005501897571553138 + }, + "Node22":{ + "Global MG94xREV":0.00559543975008409, + "Nucleotide GTR":0.005478062261613842 + }, + "Node226":{ + "Global MG94xREV":0.005594745879060948, + "Nucleotide GTR":0.005477381989095749 + }, + "Node23":{ + "Global MG94xREV":0.005618936547133832, + "Nucleotide GTR":0.005488116513150291 + }, + "Node230":{ + "Global MG94xREV":0.005586715402818173, + "Nucleotide GTR":0.005473152410546898 + }, + "Node231":{ + "Global MG94xREV":0.005573476299199454, + "Nucleotide GTR":0.00547159778188338 + }, + "Node241":{ + "Global MG94xREV":0.005574017914032298, + "Nucleotide GTR":0.005477798883065424 + }, + "Node244":{ + "Global MG94xREV":0.005631564868149991, + "Nucleotide GTR":0.005496518997143121 + }, + "Node245":{ + "Global MG94xREV":0.005641860930043722, + "Nucleotide GTR":0.005506569154539385 + }, + "Node252":{ + "Global MG94xREV":0.00560624499024505, + "Nucleotide GTR":0.005473441512665834 + }, + "Node258":{ + "Global MG94xREV":0.005593444524683299, + "Nucleotide GTR":0.005476107754690567 + }, + "Node260":{ + "Global MG94xREV":0.005565348761454758, + "Nucleotide GTR":0.005473521582621392 + }, + "Node264":{ + "Global MG94xREV":0.005591115364672502, + "Nucleotide GTR":0.005477788257690359 + }, + "Node283":{ + "Global MG94xREV":0.005594706943380021, + "Nucleotide GTR":0.005469663035826517 + }, + "Node290":{ + "Global MG94xREV":0.005591076424420491, + "Nucleotide GTR":0.005476109506909777 + }, + "Node292":{ + "Global MG94xREV":0.005558180634830368, + "Nucleotide GTR":0.00544551398387603 + }, + "Node319":{ + "Global MG94xREV":0.00563326530258351, + "Nucleotide GTR":0.005502113700459953 + }, + "Node324":{ + "Global 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name":"gb_MT326182_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CT_UW_1365_2020_Segment_null_Host_Human" + }, + "gb_MT358638_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_DEU_FFM1_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005591786722003633, + "Nucleotide GTR":0.005474004903669556, + "original name":"gb_MT358638_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_DEU_FFM1_2020_Segment_null_Host_Human" + }, + "gb_MT359866_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_ESP_VH198152683_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005589919271399852, + "Nucleotide GTR":0.005469223246210523, + "original name":"gb_MT359866_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_ESP_VH198152683_2020_Segment_null_Host_Human" + }, + "gb_MT447156_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_THA_SI200383_NT_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005594417293215322, + "Nucleotide GTR":0.005477059841797375, + "original name":"gb_MT447156_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_THA_SI200383_NT_2020_Segment_null_Host_Human" + }, + "gb_MT449654_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1063_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MT449654_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1063_2020_Segment_null_Host_Human" + }, + "gb_MT451104_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC203_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MT451104_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC203_2020_Segment_null_Host_Human" + }, + "gb_MT520188_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MGH_00184_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005643836997888733, + "Nucleotide GTR":0.005513415162685614, + "original name":"gb_MT520188_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MGH_00184_2020_Segment_null_Host_Human" + }, + "gb_MT520493_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MGH_00316_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MT520493_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MGH_00316_2020_Segment_null_Host_Human" + }, + "gb_MT601276_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_52_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005591410289624195, + "Nucleotide GTR":0.005472320917083399, + "original name":"gb_MT601276_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_52_2020_Segment_null_Host_Human" + }, + "gb_MT601281_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_67_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005699222841336904, + "Nucleotide GTR":0.005541174876424373, + "original name":"gb_MT601281_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_67_2020_Segment_null_Host_Human" + }, + "gb_MT612186_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC1576_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005585829046704516, + "Nucleotide GTR":0.005477834152100824, + "original name":"gb_MT612186_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC1576_2020_Segment_null_Host_Human" + }, + "gb_MT627613_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S260_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MT627613_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S260_2020_Segment_null_Host_Human" + }, + "gb_MT631787_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1651_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005714644211461833, + "Nucleotide GTR":0.005548568325838462, + "original name":"gb_MT631787_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1651_2020_Segment_null_Host_Human" + }, + "gb_MT641697_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC595_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MT641697_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC595_2020_Segment_null_Host_Human" + }, + "gb_MT683417_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_10131_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005593469729805412, + "Nucleotide GTR":0.005474004634873228, + "original name":"gb_MT683417_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_10131_2020_Segment_null_Host_Human" + }, + "gb_MT706153_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_32_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005577547296049738, + "Nucleotide GTR":0.005469223246210523, + "original name":"gb_MT706153_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_32_2020_Segment_null_Host_Human" + }, + "gb_MT745697_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC2124_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005628430185021072, + "Nucleotide GTR":0.005503961533125481, + "original name":"gb_MT745697_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC2124_2020_Segment_null_Host_Human" + }, + "gb_MT745746_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_SA01_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005595427368373432, + "Nucleotide GTR":0.005472484462350333, + "original name":"gb_MT745746_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_SA01_2020_Segment_null_Host_Human" + }, + "gb_MT750335_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1794_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005624635325623979, + "Nucleotide GTR":0.005504845328896214, + "original name":"gb_MT750335_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1794_2020_Segment_null_Host_Human" + }, + "gb_MT772447_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IL_UW_670_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005606808725804134, + "Nucleotide GTR":0.005476520487977195, + "original name":"gb_MT772447_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IL_UW_670_2020_Segment_null_Host_Human" + }, + "gb_MT782360_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_04172_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MT782360_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_04172_2020_Segment_null_Host_Human" + }, + "gb_MT811295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_0657_IPL_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005602779414095357, + "Nucleotide GTR":0.005483116643606682, + "original name":"gb_MT811295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_0657_IPL_2020_Segment_null_Host_Human" + }, + "gb_MT811511_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_1079_SAN_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005594934428031569, + "Nucleotide GTR":0.005477759479364592, + "original name":"gb_MT811511_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_1079_SAN_2020_Segment_null_Host_Human" + }, + "gb_MT811669_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_0155_NBG_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005608438497572238, + "Nucleotide GTR":0.005479500974163274, + "original name":"gb_MT811669_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_0155_NBG_2020_Segment_null_Host_Human" + }, + "gb_MT825091_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IRN_COVID19_IRVSH1_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005707279732364202, + "Nucleotide GTR":0.005548680261509582, + "original name":"gb_MT825091_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IRN_COVID19_IRVSH1_2020_Segment_null_Host_Human" + }, + "gb_MT834049_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S1626_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005606583852762365, 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"gb_MW490946_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2353_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MW490946_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2353_2020_Segment_null_Host_Human" + }, + "gb_MW491211_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2755_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005571456515223237, + "Nucleotide GTR":0.005473534846643134, + "original name":"gb_MW491211_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2755_2020_Segment_null_Host_Human" + }, + "gb_MW493999_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S3367_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005599041993646883, + "Nucleotide GTR":0.005479467003492122, + "original name":"gb_MW493999_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S3367_2020_Segment_null_Host_Human" + }, + "gb_MW494387_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NH_CDC_STM_A100009_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005639680120219169, + "Nucleotide GTR":0.005526708482947178, + "original name":"gb_MW494387_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NH_CDC_STM_A100009_2021_Segment_null_Host_Human" + }, + "gb_MW505295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_3142_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MW505295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_3142_2021_Segment_null_Host_Human" + }, + "gb_MW509810_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_CUNCI_HGC11I035_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005586088008998721, + "Nucleotide GTR":0.005465473449096384, + "original name":"gb_MW509810_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_CUNCI_HGC11I035_2021_Segment_null_Host_Human" + }, + "gb_MW518151_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IN_CDC_STM_A008_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005634240631758829, + "Nucleotide GTR":0.005500779085909651, + "original name":"gb_MW518151_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IN_CDC_STM_A008_2021_Segment_null_Host_Human" + }, + "gb_MW519641_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CT_CDC_STM_A100453_2021_Segment_null_Host_Human":{ + "Global 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"gb_MW523039_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_GPHL_0001_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005587898066365767, + "Nucleotide GTR":0.005470868608525645, + "original name":"gb_MW523039_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_GPHL_0001_2020_Segment_null_Host_Human" + }, + "gb_MW524907_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_RI_CDC_STM_0000013_C05_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005599551475806311, + "Nucleotide GTR":0.005472272589954402, + "original name":"gb_MW524907_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_RI_CDC_STM_0000013_C05_2021_Segment_null_Host_Human" + }, + "gb_MW528771_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3759_2021_Segment_null_Host_Human":{ + "Global 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}, + "gb_MW549223_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S3727_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005610072814509211, + "Nucleotide GTR":0.005484688677972459, + "original name":"gb_MW549223_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S3727_2020_Segment_null_Host_Human" + }, + "gb_MW549830_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2465_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MW549830_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2465_2020_Segment_null_Host_Human" + }, + "gb_MW549937_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3900_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original 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"gb_MW550458_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WY_CDC_2_3767594_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005594393610046846, + "Nucleotide GTR":0.005471472344810627, + "original name":"gb_MW550458_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WY_CDC_2_3767594_2020_Segment_null_Host_Human" + }, + "gb_MW550504_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_CDC_2_3768672_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005606730226665676, + "Nucleotide GTR":0.005481420688897495, + "original name":"gb_MW550504_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_CDC_2_3768672_2020_Segment_null_Host_Human" + }, + "gb_MW550636_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_PA_CDC_2_3768676_2020_Segment_null_Host_Human":{ + "Global 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"gb_MW560924_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_LACPHL_AF00280_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.02284509533431139, + "Nucleotide GTR":0.02236069034936522, + "original name":"gb_MW560924_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_LACPHL_AF00280_2021_Segment_null_Host_Human" + }, + "gb_MW564865_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14906_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005594417446316588, + "Nucleotide GTR":0.005477059988349209, + "original name":"gb_MW564865_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14906_2020_Segment_null_Host_Human" + }, + "gb_MW564882_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14886_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MW564882_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14886_2020_Segment_null_Host_Human" + }, + "gb_MW565403_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14413_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005628420377808867, + "Nucleotide GTR":0.00550395192954325, + "original name":"gb_MW565403_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14413_2020_Segment_null_Host_Human" + }, + "gb_MW565438_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14344_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MW565438_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14344_2020_Segment_null_Host_Human" + }, + "gb_MW565832_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0724_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005637930624046485, + "Nucleotide GTR":0.005504055374831891, + "original name":"gb_MW565832_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0724_2021_Segment_null_Host_Human" + }, + "gb_MW566477_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4490_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"gb_MW566477_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4490_2020_Segment_null_Host_Human" + }, + "gb_MW566557_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_4471_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005644974643171127, + "Nucleotide GTR":0.005507465784741251, + "original name":"gb_MW566557_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_4471_2020_Segment_null_Host_Human" + }, + "gb_MW566849_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2886_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005597894897064459, + "Nucleotide GTR":0.00547573581121221, + "original name":"gb_MW566849_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2886_2020_Segment_null_Host_Human" + }, + "gb_MW566943_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2980_2020_Segment_null_Host_Human":{ + "Global MG94xREV":0.005594439109235765, + "Nucleotide GTR":0.005477082299501769, + "original name":"gb_MW566943_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2980_2020_Segment_null_Host_Human" + }, + "gb_MW571108_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS49_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.00561060721171603, + "Nucleotide GTR":0.005482620664733259, + "original name":"gb_MW571108_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS49_2021_Segment_null_Host_Human" + }, + "gb_MW571118_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS145_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.00564497413082662, + "Nucleotide GTR":0.005507465284314313, + "original name":"gb_MW571118_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS145_2021_Segment_null_Host_Human" + }, + "gb_MW571185_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS69_2021_Segment_null_Host_Human":{ + "Global 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"gb_MW585898_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_CDC_STM_000003612_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005601622409671225, + "Nucleotide GTR":0.005469327603117374, + "original name":"gb_MW585898_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_CDC_STM_000003612_2021_Segment_null_Host_Human" + }, + "gb_MW586184_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005891_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005602458594050764, + "Nucleotide GTR":0.005472270976472237, + "original name":"gb_MW586184_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005891_2021_Segment_null_Host_Human" + }, + "gb_MW586256_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005477_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005624783848606779, + "Nucleotide GTR":0.005540564899378007, + "original name":"gb_MW586256_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005477_2021_Segment_null_Host_Human" + }, + "gb_MW586274_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_CDC_STM_000005611_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.005600641474542659, + "Nucleotide GTR":0.005470495330964893, + "original name":"gb_MW586274_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_CDC_STM_000005611_2021_Segment_null_Host_Human" + }, + "gb_MW586385_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_000005076_2021_Segment_null_Host_Human":{ + "Global MG94xREV":0.00559959639929567, + "Nucleotide GTR":0.005469223246210523, + "original 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nucleotide A to nucleotide C":0.4395430104915295, + "Substitution rate from nucleotide A to nucleotide G":1, + "Substitution rate from nucleotide A to nucleotide T":0.1216209022619113, + "Substitution rate from nucleotide C to nucleotide G":0.1952279380624755, + "Substitution rate from nucleotide C to nucleotide T":1.466497674587222, + "Substitution rate from nucleotide G to nucleotide T":0.7918204256778225 + }, + "display order":0, + "estimated parameters":359 + } + }, + "input":{ + "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/ORF6.combined.fas", + "number of sequences":177, + "number of sites":61, + "partition count":1, + "trees":{ + 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