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Update phylo example metadata to match new ingest output format
The changes made to the ingest workflow in a previous commit result in new columns of data being added to the metadata output of ingest. This commit adds those columns to the metadata of the example data in the phylogenetic workflow.
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| accession strain virus_name date region country division location length host date_released date_updated sra_accessions authors abbr_authors institution | ||
| MK161348 D8 2018-08-04 South America Brazil Boa Vista Roraima State 15894 Homo sapiens 2018-11-20 2019-04-10 Meneses,C.A.,Nascimento,V.A.,Souza,V.C.,Maito,R.M.,Gomes,M.A.,Cunha,C.R.,Antony,I.A.,Silva,M.E.,Campos,D.P.,Corado,A.L.,Pessoa,K.P.,Monteiro,D.C.,Okumoto,O.,Cunha,M.C.,Pacheco,F.C.,Naveca,F.G.,Corado,A.G. Meneses et al Instituto Leonidas e Maria Deane - Fiocruz Amazonia, Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia | ||
| MH173047 D8 2017-11-XX Europe Italy 15872 Homo sapiens 2018-06-06 2018-06-06 Marinelli,K.,Caucci,S.,Vincenzi,C.,Ferreri,M.,Magurano,F.,Bagnarelli,P.,Menzo,S. Marinelli et al Virologia, Ao Ospedali Riuniti Di Ancona | ||
| MF449469 G2V D4 2011-05-03 Europe France 15894 Homo sapiens 2017-08-28 2017-08-28 Mura,M.,Combredet,C.,Najburg,V.,Sanchez David,R.Y.,Tangy,F.,Komarova,A.V.,Sanchez-David,R.Y.,Komarova,A. Mura et al Institut Pasteur, Virology | ||
| KT732255 D8 2013-04-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service | ||
| KT732253 D8 2013-04-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service | ||
| KT732251 D8 2013-04-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service | ||
| KT732241 D8 2012-11-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service | ||
| KT732226 D4 2011-05-XX Europe United Kingdom 15684 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service | ||
| KT732223 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service | ||
| KT732221 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service | ||
| KT732220 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service | ||
| KT732219 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service | ||
| KJ755980 H1 2009-03-18 Asia China 15894 Homo sapiens 2016-05-02 2016-05-02 Jin,Q.,Xu,C.,Li,H.,Zhong,S.,Zheng,B.,Lu,Y. Jin et al Centre for Disease Control and Prevention of Zhejiang Province (ZJ CDC), Institute of Microbiology | ||
| KJ755979 H1 2008-03-20 Asia China 15894 Homo sapiens 2016-05-02 2016-05-02 Jin,Q.,Xu,C.,Li,H.,Zhong,S.,Zheng,B.,Lu,Y. Jin et al Centre for Disease Control and Prevention of Zhejiang Province (ZJ CDC), Institute of Microbiology | ||
| JN635408 2005-11-05 North America USA New Jersey 15894 Homo sapiens 2011-09-29 2012-01-26 Kirkness,E.F.,Halpin,R.,Bera,J.,Fedorova,N.,Overton,L.,Stockwell,T.,Amedeo,P.,Bishop,B.,Chen,H.,Edworthy,P.,Gupta,N.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Bankamp,B.,Byrd,L.,Bellini,W.,Rota,P. Kirkness et al J. Craig Venter Institute | ||
| JN635406 2008-03-11 North America USA Arizona 15894 Homo sapiens 2011-09-29 2012-01-26 Kirkness,E.F.,Halpin,R.,Bera,J.,Fedorova,N.,Overton,L.,Stockwell,T.,Amedeo,P.,Bishop,B.,Chen,H.,Edworthy,P.,Gupta,N.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Bankamp,B.,Byrd,L.,Bellini,W.,Rota,P. Kirkness et al J. Craig Venter Institute | ||
| FJ416067 15894 2009-05-21 2009-11-05 Zhang,Y.,Zhou,J.,Bellini,W.J.,Xu,W.,Rota,P.A.,Bamkamp,B. Zhang et al National Institute for Viral Disease Control and Prevention, China Centers for Disease Control and Prevention, WHO WPRO Regional Reference Measles Lab | ||
| EF565859 G954-PBL 1993-XX-XX Africa 6552 2008-04-02 2008-04-02 Druelle,J.,Sellin,C.I.,Waku-Kouomou,D.,Horvat,B.,Wild,F.T.,Sellin,C.,Wild,T. Druelle et al Inserm U404, Immunite et Vaccination | ||
| AB481088 1989-XX-XX Asia Japan 15894 2009-08-14 2009-08-14 Okada,H.,Itoh,M.,Nagata,K.,Takeuchi,K.,Ito,M. Okada et al Graduate School of Comprehensive Human Sciences; Tennodai 1-1-1, Tsukuba, Ibaraki 305-8575 | ||
| AB012949 9301V 15894 Homo sapiens 1998-10-19 2008-12-04 Takeda,M.,Kato,A.,Kobune,F.,Sakata,H.,Li,Y.,Shioda,T.,Sakai,Y.,Asakawa,M.,Nagai,Y. Takeda et al University of Tokyo, Viral Infection; Shirokanedai 4-6-1, Minato-ku, Tokyo 108 | ||
| accession accession_version strain virus_name date region country division location length host date_released date_updated sra_accessions authors abbr_authors institution genotype_ncbi is_reference clade coverage missing_data divergence nonACGTN QC_overall QC_missing_data QC_mixed_sites QC_rare_mutations QC_snp_clusters QC_frame_shifts QC_stop_codons frame_shifts private_reversionSubstitutions private_labeledSubstitutions private_unlabeledSubstitutions private_totalReversionSubstitutions private_totalLabeledSubstitutions private_totalUnlabeledSubstitutions private_totalPrivateSubstitutions private_SNPclusters private_totalSNPclusters | ||
| MF449469 MF449469.1 G2V Measles virus genotype D4 2011-05-03 Europe France 15894 Homo sapiens 2017-08-28 2017-08-28 Mura,M.,Combredet,C.,Najburg,V.,Sanchez David,R.Y.,Tangy,F.,Komarova,A.V.,Sanchez-David,R.Y.,Komarova,A. Mura et al Institut Pasteur, Virology D4 D4 1 0 23 0 good good good good good good good 0 0 0 0 0 | ||
| MH173047 MH173047.1 Measles virus genotype D8 2017-11-XX Europe Italy 15872 Homo sapiens 2018-06-06 2018-06-06 Marinelli,K.,Caucci,S.,Vincenzi,C.,Ferreri,M.,Magurano,F.,Bagnarelli,P.,Menzo,S. Marinelli et al Virologia, Ao Ospedali Riuniti Di Ancona D8 D8 1 0 21 0 good good good good good good good 0 0 0 0 0 | ||
| MK161348 MK161348.1 Measles virus genotype D8 2018-08-04 South America Brazil Boa Vista Roraima State 15894 Homo sapiens 2018-11-20 2019-04-10 Meneses,C.A.,Nascimento,V.A.,Souza,V.C.,Maito,R.M.,Gomes,M.A.,Cunha,C.R.,Antony,I.A.,Silva,M.E.,Campos,D.P.,Corado,A.L.,Pessoa,K.P.,Monteiro,D.C.,Okumoto,O.,Cunha,M.C.,Pacheco,F.C.,Naveca,F.G.,Corado,A.G. Meneses et al Instituto Leonidas e Maria Deane - Fiocruz Amazonia, Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia D8 D8 1 0 20 0 good good good good good good good 0 0 0 0 0 | ||
| KJ755979 KJ755979.1 Measles virus genotype H1 2008-03-20 Asia China 15894 Homo sapiens 2016-05-02 2016-05-02 Jin,Q.,Xu,C.,Li,H.,Zhong,S.,Zheng,B.,Lu,Y. Jin et al Centre for Disease Control and Prevention of Zhejiang Province (ZJ CDC), Institute of Microbiology H1 H1 1 0 38 0 good good good good good good good 0 0 0 0 0 | ||
| KJ755980 KJ755980.1 Measles virus genotype H1 2009-03-18 Asia China 15894 Homo sapiens 2016-05-02 2016-05-02 Jin,Q.,Xu,C.,Li,H.,Zhong,S.,Zheng,B.,Lu,Y. Jin et al Centre for Disease Control and Prevention of Zhejiang Province (ZJ CDC), Institute of Microbiology H1 H1 1 0 37 0 good good good good good good good 0 0 0 0 0 | ||
| KT732219 KT732219.1 Measles virus genotype B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service B3 B3 1 0 35 0 good good good good good good good 0 0 0 0 0 | ||
| KT732220 KT732220.1 Measles virus genotype B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service B3 B3 1 0 36 0 good good good good good good good G390A 0 0 1 1 0 | ||
| KT732221 KT732221.1 Measles virus genotype B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service B3 B3 1 0 35 0 good good good good good good good 0 0 0 0 0 | ||
| KT732223 KT732223.1 Measles virus genotype B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service B3 B3 1 0 35 0 good good good good good good good 0 0 0 0 0 | ||
| KT732226 KT732226.1 Measles virus genotype D4 2011-05-XX Europe United Kingdom 15684 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service D4 D4 1 0 23 0 good good good good good good good 0 0 0 0 0 | ||
| KT732241 KT732241.1 Measles virus genotype D8 2012-11-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service D8 D8 1 0 25 0 good good good good good good good 0 0 0 0 0 | ||
| KT732251 KT732251.1 Measles virus genotype D8 2013-04-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service D8 D8 1 0 26 0 good good good good good good good G90A 0 0 1 1 0 | ||
| KT732253 KT732253.1 Measles virus genotype D8 2013-04-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service D8 D8 1 0 25 0 good good good good good good good 0 0 0 0 0 | ||
| KT732255 KT732255.1 Measles virus genotype D8 2013-04-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service D8 D8 1 0 26 0 good good good good good good good G90A 0 0 1 1 0 | ||
| FJ416067 FJ416067.1 Measles morbillivirus 15894 2009-05-21 2009-11-05 Zhang,Y.,Zhou,J.,Bellini,W.J.,Xu,W.,Rota,P.A.,Bamkamp,B. Zhang et al National Institute for Viral Disease Control and Prevention, China Centers for Disease Control and Prevention, WHO WPRO Regional Reference Measles Lab A 1 0 28 0 good good good good good good good 0 0 0 0 0 | ||
| JN635406 JN635406.1 Measles virus strain MVi/Arizona.USA/11.08/2 2008-XX-XX North America USA Arizona 15894 Homo sapiens 2011-09-29 2012-01-26 Kirkness,E.F.,Halpin,R.,Bera,J.,Fedorova,N.,Overton,L.,Stockwell,T.,Amedeo,P.,Bishop,B.,Chen,H.,Edworthy,P.,Gupta,N.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Bankamp,B.,Byrd,L.,Bellini,W.,Rota,P. Kirkness et al J. Craig Venter Institute D5 1 0 12 0 good good good good good good good 0 0 0 0 0 | ||
| JN635408 JN635408.1 Measles virus strain MVi/New Jersey.USA/45.05 2005-XX-XX North America USA New Jersey 15894 Homo sapiens 2011-09-29 2012-01-26 Kirkness,E.F.,Halpin,R.,Bera,J.,Fedorova,N.,Overton,L.,Stockwell,T.,Amedeo,P.,Bishop,B.,Chen,H.,Edworthy,P.,Gupta,N.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Bankamp,B.,Byrd,L.,Bellini,W.,Rota,P. Kirkness et al J. Craig Venter Institute B3 1 0 32 0 good good good good good good good 0 0 0 0 0 | ||
| AB012949 AB012949.1 9301V Measles morbillivirus 15894 Homo sapiens 1998-10-19 2008-12-04 Takeda,M.,Kato,A.,Kobune,F.,Sakata,H.,Li,Y.,Shioda,T.,Sakai,Y.,Asakawa,M.,Nagai,Y. Takeda et al University of Tokyo, Viral Infection; Shirokanedai 4-6-1, Minato-ku, Tokyo 108 D5 1 0 13 0 good good good good good good good G373A 0 0 1 1 0 | ||
| AB481088 AB481088.1 Measles morbillivirus 1989-XX-XX Asia Japan 15894 2009-08-14 2009-08-14 Okada,H.,Itoh,M.,Nagata,K.,Takeuchi,K.,Ito,M. Okada et al Graduate School of Comprehensive Human Sciences; Tennodai 1-1-1, Tsukuba, Ibaraki 305-8575 D3 1 0 1 0 good good good good good good good C186T,A202G,T357C A421G 3 0 1 4 0 | ||
| EF565859 EF565859.1 G954-PBL Measles morbillivirus Africa 6552 2008-04-02 2008-04-02 Druelle,J.,Sellin,C.I.,Waku-Kouomou,D.,Horvat,B.,Wild,F.T.,Sellin,C.,Wild,T. Druelle et al Inserm U404, Immunite et Vaccination |
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