From 4598e5a2e23ae87b19fca98466882455f1f33afe Mon Sep 17 00:00:00 2001 From: Albert Tian Chen Date: Mon, 1 May 2023 02:20:29 -0400 Subject: [PATCH] New flu subtypes (H5NX, H7NX, H9NX) (#620) * Add new subtypes: H5NX, H7NX, H9NX. Also, add putative signal peptides for B subtypes (B-vic, B-yam) * Update flu ingest structure * Use configurable min_date for global_seq_data analysis * Shorten sequence mutation table name to accomodate longer partition names * Add new subtypes to flu config files --- config/config_flu_genbank.yaml | 9 + config/config_flu_gisaid.yaml | 9 + config/config_flu_gisaid_dev.yaml | 9 + services/server/cg_server/db_seed/seed.py | 4 +- .../flu/alignments/B-vic_4_FLBHAAA.dna | Bin 23727 -> 24284 bytes .../flu/alignments/B-yam_4_MK715607.dna | Bin 25887 -> 26445 bytes .../flu/alignments/H5N1_1_NC_007357.dna | Bin 0 -> 24458 bytes .../flu/alignments/H5N1_2_NC_007358.dna | Bin 0 -> 26160 bytes .../flu/alignments/H5N1_3_NC_007359.dna | Bin 0 -> 25884 bytes .../flu/alignments/H5N1_4_NC_007362.dna | Bin 0 -> 23455 bytes .../flu/alignments/H5N1_5_NC_007360.dna | Bin 0 -> 21179 bytes .../flu/alignments/H5N1_6_NC_007361.dna | Bin 0 -> 20744 bytes .../flu/alignments/H5N1_7_NC_007363.dna | Bin 0 -> 20412 bytes .../flu/alignments/H5N1_8_NC_007364.dna | Bin 0 -> 19617 bytes .../flu/alignments/H7N2_1_NC_026422.dna | Bin 0 -> 25596 bytes .../flu/alignments/H7N2_2_NC_026423.dna | Bin 0 -> 26990 bytes .../flu/alignments/H7N2_3_NC_026424.dna | Bin 0 -> 26756 bytes .../flu/alignments/H7N2_4_NC_026425.dna | Bin 0 -> 24367 bytes .../flu/alignments/H7N2_5_NC_026426.dna | Bin 0 -> 22258 bytes .../flu/alignments/H7N2_6_NC_026429.dna | Bin 0 -> 21758 bytes .../flu/alignments/H7N2_7_NC_026427.dna | Bin 0 -> 21196 bytes .../flu/alignments/H7N2_8_NC_026428.dna | Bin 0 -> 20797 bytes .../flu/alignments/H9N2_1_NC_004910.dna | Bin 0 -> 24723 bytes .../flu/alignments/H9N2_2_NC_004911.dna | Bin 0 -> 25319 bytes .../flu/alignments/H9N2_3_NC_004912.dna | Bin 0 -> 24393 bytes .../flu/alignments/H9N2_4_NC_004908.dna | Bin 0 -> 22827 bytes .../flu/alignments/H9N2_5_NC_004905.dna | Bin 0 -> 22066 bytes .../flu/alignments/H9N2_6_NC_004909.dna | Bin 0 -> 20734 bytes .../flu/alignments/H9N2_7_NC_004907.dna | Bin 0 -> 21908 bytes .../flu/alignments/H9N2_8_NC_004906.dna | Bin 0 -> 21632 bytes static_data/flu/alignments/HA_all.praln | Bin 0 -> 9404 bytes static_data/flu/genes.csv | 18 +- static_data/flu/genes_processed.json | 435 ++++++++++++++++-- .../H5NX/A-Goose-Guangdong-1-96/1.fa | 31 ++ .../H5NX/A-Goose-Guangdong-1-96/2.fa | 31 ++ .../H5NX/A-Goose-Guangdong-1-96/3.fa | 29 ++ .../H5NX/A-Goose-Guangdong-1-96/4.fa | 23 + .../H5NX/A-Goose-Guangdong-1-96/5.fa | 21 + .../H5NX/A-Goose-Guangdong-1-96/6.fa | 20 + .../H5NX/A-Goose-Guangdong-1-96/7.fa | 14 + .../H5NX/A-Goose-Guangdong-1-96/8.fa | 12 + .../H5NX/A-Goose-Guangdong-1-96/DESCRIPTION | 1 + .../H5NX/A-Goose-Guangdong-1-96/NOTES | 29 ++ .../H7NX/A-Shanghai-02-2013/1.fa | 30 ++ .../H7NX/A-Shanghai-02-2013/2.fa | 30 ++ .../H7NX/A-Shanghai-02-2013/3.fa | 29 ++ .../H7NX/A-Shanghai-02-2013/4.fa | 23 + .../H7NX/A-Shanghai-02-2013/5.fa | 20 + .../H7NX/A-Shanghai-02-2013/6.fa | 19 + .../H7NX/A-Shanghai-02-2013/7.fa | 14 + .../H7NX/A-Shanghai-02-2013/8.fa | 12 + .../H7NX/A-Shanghai-02-2013/DESCRIPTION | 1 + .../H7NX/A-Shanghai-02-2013/NOTES | 25 + .../H9NX/A-Hong-Kong-1073-99/1.fa | 31 ++ .../H9NX/A-Hong-Kong-1073-99/2.fa | 31 ++ .../H9NX/A-Hong-Kong-1073-99/3.fa | 29 ++ .../H9NX/A-Hong-Kong-1073-99/4.fa | 23 + .../H9NX/A-Hong-Kong-1073-99/5.fa | 21 + .../H9NX/A-Hong-Kong-1073-99/6.fa | 19 + .../H9NX/A-Hong-Kong-1073-99/7.fa | 14 + .../H9NX/A-Hong-Kong-1073-99/8.fa | 13 + .../H9NX/A-Hong-Kong-1073-99/NOTES | 30 ++ static_data/flu/proteins.csv | 18 +- static_data/flu/proteins_processed.json | 435 ++++++++++++++++-- static_data/flu/reference.json | 141 ++++++ workflow_flu_gisaid_ingest/Snakefile | 12 +- .../scripts/clean_metadata.py | 8 + workflow_main/analyses/Snakefile | 2 + .../analyses/scripts/global_seq_data.py | 5 +- 69 files changed, 1613 insertions(+), 117 deletions(-) create mode 100644 static_data/flu/alignments/H5N1_1_NC_007357.dna create mode 100644 static_data/flu/alignments/H5N1_2_NC_007358.dna create mode 100644 static_data/flu/alignments/H5N1_3_NC_007359.dna create mode 100644 static_data/flu/alignments/H5N1_4_NC_007362.dna create mode 100644 static_data/flu/alignments/H5N1_5_NC_007360.dna create mode 100644 static_data/flu/alignments/H5N1_6_NC_007361.dna create mode 100644 static_data/flu/alignments/H5N1_7_NC_007363.dna create mode 100644 static_data/flu/alignments/H5N1_8_NC_007364.dna create mode 100644 static_data/flu/alignments/H7N2_1_NC_026422.dna create mode 100644 static_data/flu/alignments/H7N2_2_NC_026423.dna create mode 100644 static_data/flu/alignments/H7N2_3_NC_026424.dna create mode 100644 static_data/flu/alignments/H7N2_4_NC_026425.dna create mode 100644 static_data/flu/alignments/H7N2_5_NC_026426.dna create mode 100644 static_data/flu/alignments/H7N2_6_NC_026429.dna create mode 100644 static_data/flu/alignments/H7N2_7_NC_026427.dna create mode 100644 static_data/flu/alignments/H7N2_8_NC_026428.dna create mode 100644 static_data/flu/alignments/H9N2_1_NC_004910.dna create mode 100644 static_data/flu/alignments/H9N2_2_NC_004911.dna create mode 100644 static_data/flu/alignments/H9N2_3_NC_004912.dna create mode 100644 static_data/flu/alignments/H9N2_4_NC_004908.dna create mode 100644 static_data/flu/alignments/H9N2_5_NC_004905.dna create mode 100644 static_data/flu/alignments/H9N2_6_NC_004909.dna create mode 100644 static_data/flu/alignments/H9N2_7_NC_004907.dna create mode 100644 static_data/flu/alignments/H9N2_8_NC_004906.dna create mode 100644 static_data/flu/alignments/HA_all.praln create mode 100644 static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/1.fa create mode 100644 static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/2.fa create mode 100644 static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/3.fa create mode 100644 static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/4.fa create mode 100644 static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/5.fa create mode 100644 static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/6.fa create mode 100644 static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/7.fa create mode 100644 static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/8.fa create mode 100644 static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/DESCRIPTION create mode 100644 static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/NOTES create mode 100644 static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/1.fa create mode 100644 static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/2.fa create mode 100644 static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/3.fa create mode 100644 static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/4.fa create mode 100644 static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/5.fa create mode 100644 static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/6.fa create mode 100644 static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/7.fa create mode 100644 static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/8.fa create mode 100644 static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/DESCRIPTION create mode 100644 static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/NOTES create mode 100644 static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/1.fa create mode 100644 static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/2.fa create mode 100644 static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/3.fa create mode 100644 static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/4.fa create mode 100644 static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/5.fa create mode 100644 static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/6.fa create mode 100644 static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/7.fa create mode 100644 static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/8.fa create mode 100644 static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/NOTES diff --git a/config/config_flu_genbank.yaml b/config/config_flu_genbank.yaml index 118f4d3f..2f348759 100644 --- a/config/config_flu_genbank.yaml +++ b/config/config_flu_genbank.yaml @@ -80,6 +80,9 @@ report_group_references: B-yam: B-Phuket-3073-2013 H1N1: A-Wisconsin-67-2022 H3N2: A-Darwin-6-2021 + H5NX: A-Goose-Guangdong-1-96 + H7NX: A-Shanghai-02-2013 + H9NX: A-Hong-Kong-1073-99 # Surveillance plot options # see: workflow_main/scripts/surveillance.py @@ -95,6 +98,9 @@ surv_group_references: B-yam: B-Phuket-3073-2013 H1N1: A-Wisconsin-67-2022 H3N2: A-Darwin-6-2021 + H5NX: A-Goose-Guangdong-1-96 + H7NX: A-Shanghai-02-2013 + H9NX: A-Hong-Kong-1073-99 # --------------- # DATABASE @@ -134,6 +140,9 @@ default_references: B-yam: B-Phuket-3073-2013 H1N1: A-Wisconsin-67-2022 H3N2: A-Darwin-6-2021 + H5NX: A-Goose-Guangdong-1-96 + H7NX: A-Shanghai-02-2013 + H9NX: A-Hong-Kong-1073-99 # Home page show_home_banner: false diff --git a/config/config_flu_gisaid.yaml b/config/config_flu_gisaid.yaml index af7191fb..a33adac7 100644 --- a/config/config_flu_gisaid.yaml +++ b/config/config_flu_gisaid.yaml @@ -84,6 +84,9 @@ report_group_references: B-yam: B-Phuket-3073-2013 H1N1: A-Wisconsin-67-2022 H3N2: A-Darwin-6-2021 + H5NX: A-Goose-Guangdong-1-96 + H7NX: A-Shanghai-02-2013 + H9NX: A-Hong-Kong-1073-99 # Surveillance plot options # see: workflow_main/scripts/surveillance.py @@ -99,6 +102,9 @@ surv_group_references: B-yam: B-Phuket-3073-2013 H1N1: A-Wisconsin-67-2022 H3N2: A-Darwin-6-2021 + H5NX: A-Goose-Guangdong-1-96 + H7NX: A-Shanghai-02-2013 + H9NX: A-Hong-Kong-1073-99 # --------------- # DATABASE @@ -139,6 +145,9 @@ default_references: B-yam: B-Phuket-3073-2013 H1N1: A-Wisconsin-67-2022 H3N2: A-Darwin-6-2021 + H5NX: A-Goose-Guangdong-1-96 + H7NX: A-Shanghai-02-2013 + H9NX: A-Hong-Kong-1073-99 # Home page show_home_banner: false diff --git a/config/config_flu_gisaid_dev.yaml b/config/config_flu_gisaid_dev.yaml index bd579eaf..7c42bd85 100644 --- a/config/config_flu_gisaid_dev.yaml +++ b/config/config_flu_gisaid_dev.yaml @@ -84,6 +84,9 @@ report_group_references: B-yam: B-Phuket-3073-2013 H1N1: A-Wisconsin-67-2022 H3N2: A-Darwin-6-2021 + H5NX: A-Goose-Guangdong-1-96 + H7NX: A-Shanghai-02-2013 + H9NX: A-Hong-Kong-1073-99 # Surveillance plot options # see: workflow_main/scripts/surveillance.py @@ -99,6 +102,9 @@ surv_group_references: B-yam: B-Phuket-3073-2013 H1N1: A-Wisconsin-67-2022 H3N2: A-Darwin-6-2021 + H5NX: A-Goose-Guangdong-1-96 + H7NX: A-Shanghai-02-2013 + H9NX: A-Hong-Kong-1073-99 # --------------- # DATABASE @@ -139,6 +145,9 @@ default_references: B-yam: B-Phuket-3073-2013 H1N1: A-Wisconsin-67-2022 H3N2: A-Darwin-6-2021 + H5NX: A-Goose-Guangdong-1-96 + H7NX: A-Shanghai-02-2013 + H9NX: A-Hong-Kong-1073-99 # Home page show_home_banner: false diff --git a/services/server/cg_server/db_seed/seed.py b/services/server/cg_server/db_seed/seed.py index 1e262fde..2767a62b 100644 --- a/services/server/cg_server/db_seed/seed.py +++ 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zeZWoqitSXuVpmtNdT$?I#$sD_tTo$uA*-?Nx=L0X?rpVwHr1?|Z9CMnHfrnTEU@ik zl(Sf`XZ7Q{qNv5*s%o(-%38e-{I^}+V(0ZOcA>!48*i#yY^O38LwtWlovZhDZLy18 zR_$V22_1AolxLcNR*%yf$we{i{)OMjb)&)0L z$hz8gERwNaCF>7gQ7U8GwKDdeVi`J8y|cM!)|_;%nlZ5LLfs6lHl;JRQ|%0XdsXqQ zkGMkx4U@R4hQ_vvXzV>zGz|Bd7Sh&i+o_iJa}+;nD}{UlKUpjmKm2EVB72w}{+5fq b_6t9IdnbEGi@hK4)2F>RjbZ-ell=d`jq*9< literal 0 HcmV?d00001 diff --git a/static_data/flu/genes.csv b/static_data/flu/genes.csv index f81af438..969b1bad 100644 --- a/static_data/flu/genes.csv +++ b/static_data/flu/genes.csv @@ -130,7 +130,7 @@ H5NX,A-Goose-Guangdong-1-96,NS1,8,15..707,1,0,[], H7NX,A-Shanghai-02-2013,PB2,1,1..2280,1,0,[], H7NX,A-Shanghai-02-2013,PB1,2,1..2274,1,0,[], H7NX,A-Shanghai-02-2013,PA,3,1..2151,1,0,[], -H7NX,A-Shanghai-02-2013,HA,4,1..1683,1,16,"[{""name"": ""signal peptide"", ""ranges"": [[1, 18]]}, {""name"": ""HA1"", ""ranges"": [[19, 339]]}, {""name"": ""HA2"", ""ranges"": [[340, 560]]}]", +H7NX,A-Shanghai-02-2013,HA,4,1..1683,1,18,"[{""name"": ""signal peptide"", ""ranges"": [[1, 18]]}, {""name"": ""HA1"", ""ranges"": [[19, 339]]}, {""name"": ""HA2"", ""ranges"": [[340, 560]]}]", H7NX,A-Shanghai-02-2013,NP,5,1..1497,1,0,[], H7NX,A-Shanghai-02-2013,NA,6,1..1398,1,0,[], H7NX,A-Shanghai-02-2013,M1,7,1..759,1,0,[], @@ -140,14 +140,14 @@ H7NX,A-Shanghai-02-2013,NS1,8,1..654,1,0,[], H9NX,A-Hong-Kong-1073-99,PB2,1,28..2307,1,0,[], H9NX,A-Hong-Kong-1073-99,PB1,2,24..2300,1,0,[], H9NX,A-Hong-Kong-1073-99,PA,3,21..2171,1,0,[], -H9NX,A-Hong-Kong-1073-99,HA,4,1..1714,1,16,"[{""name"": ""signal peptide"", ""ranges"": [[1, 18]]}, {""name"": ""HA1"", ""ranges"": [[19, 338]]}, {""name"": ""HA2"", ""ranges"": [[339, 560]]}]", +H9NX,A-Hong-Kong-1073-99,HA,4,1..1714,1,18,"[{""name"": ""signal peptide"", ""ranges"": [[1, 18]]}, {""name"": ""HA1"", ""ranges"": [[19, 338]]}, {""name"": ""HA2"", ""ranges"": [[339, 560]]}]", H9NX,A-Hong-Kong-1073-99,NP,5,40..1536,1,0,[], H9NX,A-Hong-Kong-1073-99,NA,6,1..1404,1,0,[], H9NX,A-Hong-Kong-1073-99,M1,7,33..791,1,0,[], H9NX,A-Hong-Kong-1073-99,M2,7,33..59;748..1014,1,0,[], H9NX,A-Hong-Kong-1073-99,NEP,8,27..56;529..864,1,0,[], H9NX,A-Hong-Kong-1073-99,NS1,8,27..719,1,0,[], -B-yam,B-Massachusetts-02-2012,HA,4,1..1755,1,0,[], +B-yam,B-Massachusetts-02-2012,HA,4,1..1755,1,15,"[{""name"": ""signal peptide"", ""ranges"": [[1, 15]]}, {""name"": ""HA1"", ""ranges"": [[16, 361]]}, {""name"": ""HA2"", ""ranges"": [[362, 584]]}]", B-yam,B-Massachusetts-02-2012,NA,6,1..1401,1,0,[], B-yam,B-Massachusetts-02-2012,NB,6,3..296,1,0,[], B-yam,B-Massachusetts-02-2012,NEP,8,1..33;689..1024,1,0,[], @@ -155,7 +155,7 @@ B-yam,B-Massachusetts-02-2012,NS1,8,1..846,1,0,[], B-yam,B-Phuket-3073-2013,PB2,1,1..2313,1,0,[], B-yam,B-Phuket-3073-2013,PB1,2,1..2259,1,0,[], B-yam,B-Phuket-3073-2013,PA,3,1..2181,1,0,[], -B-yam,B-Phuket-3073-2013,HA,4,1..1755,1,0,[], +B-yam,B-Phuket-3073-2013,HA,4,1..1755,1,15,"[{""name"": ""signal peptide"", ""ranges"": [[1, 15]]}, {""name"": ""HA1"", ""ranges"": [[16, 361]]}, {""name"": ""HA2"", ""ranges"": [[362, 584]]}]", B-yam,B-Phuket-3073-2013,NP,5,1..1683,1,0,[], B-yam,B-Phuket-3073-2013,NA,6,34..1434,1,0,[], B-yam,B-Phuket-3073-2013,NB,6,27..329,1,0,[], @@ -163,7 +163,7 @@ B-yam,B-Phuket-3073-2013,M,7,1..747,1,0,[], B-yam,B-Phuket-3073-2013,BM2,7,747..1076,1,0,[], B-yam,B-Phuket-3073-2013,NEP,8,1..33;689..1024,1,0,[], B-yam,B-Phuket-3073-2013,NS1,8,1..846,1,0,[], -B-yam,B-Wisconsin-01-2010,HA,4,1..1755,1,0,[], +B-yam,B-Wisconsin-01-2010,HA,4,1..1755,1,15,"[{""name"": ""signal peptide"", ""ranges"": [[1, 15]]}, {""name"": ""HA1"", ""ranges"": [[16, 361]]}, {""name"": ""HA2"", ""ranges"": [[362, 584]]}]", B-yam,B-Wisconsin-01-2010,NA,6,1..1401,1,0,[], B-yam,B-Wisconsin-01-2010,NB,6,3..296,1,0,[], B-yam,B-Wisconsin-01-2010,NEP,8,1..33;689..1024,1,0,[], @@ -171,7 +171,7 @@ B-yam,B-Wisconsin-01-2010,NS1,8,1..846,1,0,[], B-vic,B-Austria-1359417-2021,PB2,1,1..2313,1,0,[], B-vic,B-Austria-1359417-2021,PB1,2,1..2259,1,0,[], B-vic,B-Austria-1359417-2021,PA,3,1..2181,1,0,[], -B-vic,B-Austria-1359417-2021,HA,4,1..1749,1,0,[], +B-vic,B-Austria-1359417-2021,HA,4,1..1749,1,15,"[{""name"": ""signal peptide"", ""ranges"": [[1, 15]]}, {""name"": ""HA1"", ""ranges"": [[16, 359]]}, {""name"": ""HA2"", ""ranges"": [[360, 582]]}]", B-vic,B-Austria-1359417-2021,NP,5,1..1683,1,0,[], B-vic,B-Austria-1359417-2021,NA,6,8..1408,1,0,[], B-vic,B-Austria-1359417-2021,NB,6,1..303,1,0,[], @@ -179,8 +179,8 @@ B-vic,B-Austria-1359417-2021,M,7,1..747,1,0,[], B-vic,B-Austria-1359417-2021,BM2,7,747..1076,1,0,[], B-vic,B-Austria-1359417-2021,NEP,8,1..36;692..1027,1,0,[], B-vic,B-Austria-1359417-2021,NS1,8,1..849,1,0,[], -B-vic,B-Brisbane-60-2008,HA,4,34..1791,1,0,[], -B-vic,B-Colorado-06-2017,HA,4,34..1785,1,0,[], +B-vic,B-Brisbane-60-2008,HA,4,34..1791,1,15,"[{""name"": ""signal peptide"", ""ranges"": [[1, 15]]}, {""name"": ""HA1"", ""ranges"": [[16, 362]]}, {""name"": ""HA2"", ""ranges"": [[363, 585]]}]", +B-vic,B-Colorado-06-2017,HA,4,34..1785,1,15,"[{""name"": ""signal peptide"", ""ranges"": [[1, 15]]}, {""name"": ""HA1"", ""ranges"": [[16, 360]]}, {""name"": ""HA2"", ""ranges"": [[361, 583]]}]", B-vic,B-Colorado-06-2017,NA,6,54..1454,1,0,[], B-vic,B-Colorado-06-2017,NB,6,47..349,1,0,[], B-vic,B-Colorado-06-2017,M,7,25..771,1,0,[], @@ -188,7 +188,7 @@ B-vic,B-Colorado-06-2017,BM2,7,771..1100,1,0,[], B-vic,B-Washington-02-2019,PB2,1,10..2322,1,0,[], B-vic,B-Washington-02-2019,PB1,2,8..2266,1,0,[], B-vic,B-Washington-02-2019,PA,3,16..2196,1,0,[], -B-vic,B-Washington-02-2019,HA,4,20..1768,1,0,[], +B-vic,B-Washington-02-2019,HA,4,20..1768,1,15,"[{""name"": ""signal peptide"", ""ranges"": [[1, 15]]}, {""name"": ""HA1"", ""ranges"": [[16, 359]]}, {""name"": ""HA2"", ""ranges"": [[360, 582]]}]", B-vic,B-Washington-02-2019,NP,5,47..1729,1,0,[], B-vic,B-Washington-02-2019,NA,6,40..1440,1,0,[], B-vic,B-Washington-02-2019,NB,6,33..335,1,0,[], diff --git a/static_data/flu/genes_processed.json b/static_data/flu/genes_processed.json index aa2f79a1..e1735459 100644 --- a/static_data/flu/genes_processed.json +++ b/static_data/flu/genes_processed.json @@ -6036,14 +6036,14 @@ ] ], "protein_coding": true, - "residue_offset": 16, + "residue_offset": 18, "domains": [ { "name": "signal peptide", "ranges": [ [ - -15, - 2 + -17, + 0 ] ], "row": 0, @@ -6058,8 +6058,8 @@ "name": "HA1", "ranges": [ [ - 3, - 323 + 1, + 321 ] ], "row": 1, @@ -6074,8 +6074,8 @@ "name": "HA2", "ranges": [ [ - 324, - 544 + 322, + 542 ] ], "row": 0, @@ -6091,8 +6091,8 @@ "len_nt": 1683, "len_aa": 561, "residue_offset_range": [ - -15, - 545 + -17, + 543 ], "nt_range": [ 1, @@ -6481,14 +6481,14 @@ ] ], "protein_coding": true, - "residue_offset": 16, + "residue_offset": 18, "domains": [ { "name": "signal peptide", "ranges": [ [ - -15, - 2 + -17, + 0 ] ], "row": 0, @@ -6503,8 +6503,8 @@ "name": "HA1", "ranges": [ [ - 3, - 322 + 1, + 320 ] ], "row": 1, @@ -6519,8 +6519,8 @@ "name": "HA2", "ranges": [ [ - 323, - 544 + 321, + 542 ] ], "row": 0, @@ -6536,8 +6536,8 @@ "len_nt": 1714, "len_aa": 571, "residue_offset_range": [ - -15, - 555 + -17, + 553 ], "nt_range": [ 1, @@ -6815,14 +6815,63 @@ ] ], "protein_coding": true, - "residue_offset": 0, - "domains": [], + "residue_offset": 15, + "domains": [ + { + "name": "signal peptide", + "ranges": [ + [ + -14, + 0 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1, + 45 + ] + ] + }, + { + "name": "HA1", + "ranges": [ + [ + 1, + 346 + ] + ], + "row": 1, + "nt_ranges": [ + [ + 46, + 1083 + ] + ] + }, + { + "name": "HA2", + "ranges": [ + [ + 347, + 569 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1084, + 1752 + ] + ] + } + ], "notes": "", "len_nt": 1755, "len_aa": 585, "residue_offset_range": [ - 1, - 585 + -14, + 570 ], "nt_range": [ 1, @@ -7125,14 +7174,63 @@ ] ], "protein_coding": true, - "residue_offset": 0, - "domains": [], + "residue_offset": 15, + "domains": [ + { + "name": "signal peptide", + "ranges": [ + [ + -14, + 0 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1, + 45 + ] + ] + }, + { + "name": "HA1", + "ranges": [ + [ + 1, + 346 + ] + ], + "row": 1, + "nt_ranges": [ + [ + 46, + 1083 + ] + ] + }, + { + "name": "HA2", + "ranges": [ + [ + 347, + 569 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1084, + 1752 + ] + ] + } + ], "notes": "", "len_nt": 1755, "len_aa": 585, "residue_offset_range": [ - 1, - 585 + -14, + 570 ], "nt_range": [ 1, @@ -7435,14 +7533,63 @@ ] ], "protein_coding": true, - "residue_offset": 0, - "domains": [], + "residue_offset": 15, + "domains": [ + { + "name": "signal peptide", + "ranges": [ + [ + -14, + 0 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1, + 45 + ] + ] + }, + { + "name": "HA1", + "ranges": [ + [ + 1, + 346 + ] + ], + "row": 1, + "nt_ranges": [ + [ + 46, + 1083 + ] + ] + }, + { + "name": "HA2", + "ranges": [ + [ + 347, + 569 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1084, + 1752 + ] + ] + } + ], "notes": "", "len_nt": 1755, "len_aa": 585, "residue_offset_range": [ - 1, - 585 + -14, + 570 ], "nt_range": [ 1, @@ -7745,14 +7892,63 @@ ] ], "protein_coding": true, - "residue_offset": 0, - "domains": [], + "residue_offset": 15, + "domains": [ + { + "name": "signal peptide", + "ranges": [ + [ + -14, + 0 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1, + 45 + ] + ] + }, + { + "name": "HA1", + "ranges": [ + [ + 1, + 344 + ] + ], + "row": 1, + "nt_ranges": [ + [ + 46, + 1077 + ] + ] + }, + { + "name": "HA2", + "ranges": [ + [ + 345, + 567 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1078, + 1746 + ] + ] + } + ], "notes": "", "len_nt": 1749, "len_aa": 583, "residue_offset_range": [ - 1, - 583 + -14, + 568 ], "nt_range": [ 1, @@ -8055,14 +8251,63 @@ ] ], "protein_coding": true, - "residue_offset": 0, - "domains": [], + "residue_offset": 15, + "domains": [ + { + "name": "signal peptide", + "ranges": [ + [ + -14, + 0 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 34, + 78 + ] + ] + }, + { + "name": "HA1", + "ranges": [ + [ + 1, + 347 + ] + ], + "row": 1, + "nt_ranges": [ + [ + 79, + 1119 + ] + ] + }, + { + "name": "HA2", + "ranges": [ + [ + 348, + 570 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1120, + 1788 + ] + ] + } + ], "notes": "", "len_nt": 1758, "len_aa": 586, "residue_offset_range": [ - 1, - 586 + -14, + 571 ], "nt_range": [ 34, @@ -8094,14 +8339,63 @@ ] ], "protein_coding": true, - "residue_offset": 0, - "domains": [], + "residue_offset": 15, + "domains": [ + { + "name": "signal peptide", + "ranges": [ + [ + -14, + 0 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 34, + 78 + ] + ] + }, + { + "name": "HA1", + "ranges": [ + [ + 1, + 345 + ] + ], + "row": 1, + "nt_ranges": [ + [ + 79, + 1113 + ] + ] + }, + { + "name": "HA2", + "ranges": [ + [ + 346, + 568 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1114, + 1782 + ] + ] + } + ], "notes": "", "len_nt": 1752, "len_aa": 584, "residue_offset_range": [ - 1, - 584 + -14, + 569 ], "nt_range": [ 34, @@ -8392,14 +8686,63 @@ ] ], "protein_coding": true, - "residue_offset": 0, - "domains": [], + "residue_offset": 15, + "domains": [ + { + "name": "signal peptide", + "ranges": [ + [ + -14, + 0 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 20, + 64 + ] + ] + }, + { + "name": "HA1", + "ranges": [ + [ + 1, + 344 + ] + ], + "row": 1, + "nt_ranges": [ + [ + 65, + 1096 + ] + ] + }, + { + "name": "HA2", + "ranges": [ + [ + 345, + 567 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1097, + 1765 + ] + ] + } + ], "notes": "", "len_nt": 1749, "len_aa": 583, "residue_offset_range": [ - 1, - 583 + -14, + 568 ], "nt_range": [ 20, diff --git a/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/1.fa b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/1.fa new file mode 100644 index 00000000..2813eba1 --- /dev/null +++ b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/1.fa @@ -0,0 +1,31 @@ +>5779|A/Goose/Guangdong/1/96|EPI_ISL_1254|PB2|| +agcaaaagcaggtcaattatattcaatatggaaagaataaaagaactaagagatctaatgtcgcagtcccgcactcgcga +gatactaacaaaaaccactgtggatcatatggccataatcaagaaatacacatcaggaagacaagagaagaaccctgctc +tcagaatgaaatggatgatggcaatgaaatatccaatcacagcagacaagagaataatggagatgattcctgaaaggaat +gagcaaggacaaacgctttggagcaagacaaatgatgctgggtcggacagagtgatggtgtctcccctagctgtaacttg +gtggaacaggaatgggccgacaacaagtacagtccattatccaaaggtttacaaaacatactttgagaaggttgaaaggt +taaaacatggaaccttcggtcccgttcatttccgaaaccaagttaaaatacgtcgccgggtggatataaacccgggccat +gcagatctcagtgctaaagaagcacaagatgttatcatggaggtcgttttcccaaatgaagtgggagctagaatattgac +atcagagtcgcaattgacaataacaaaagagaagaaagaagagctccaggattgtaaaattgctcctttaatggtggcat +acatgttggaaagagaactggtccgcaaaaccagatttctaccggtagcaggcggaacaagcagtgtgtacattgaggta +ttgcatttgactcaagggacctgttgggaacagatgtacactcccggcggagaagtaagaaatgatgatgttgaccagag +tttgatcatcgctgccagaaacattgttaggagagcaacagtatcagcggacccactggcatcactcttggagatgtgtc +acagcacacaaattgggggaataaggatggtggacatccttaggcaaaacccaactgaggagcaagctgtggatatatgc +aaagcagcaatgggtttgaggatcagttcatcctttagctttggaggcttcactttcaaaagaacaaatggatcatccgt +caagaaggaagaggaagtgcttacaggcaacctccaaacattgaaaataaaagtacatgaggggtatgaagaattcacaa +tggttgggcggagagcaacagctatcctgaggaaagcaactagaaggctgattcagttgatagtaagtggaagagatgaa +caatcaatcgctgaagcgatcattgtagcaatggtgttctcacaggaggattgcatgataaaggcagtccgaggcgatct +gaatttcgtgaacagagcaaaccaaagattgaaccccatgcatcaactcctgaggcacttccaaaaagatgcaaaagtgc +tgtttcagaactggggaattgaacctattgacaatgtcatggggatgatcggaatattacctgacatgactccaagcgca +gagatgtcactgagaggagtgagagttagtaagatgggagtagatgaatattccagcacggagagagtggtggtgagtat +tgaccgtttcttgagggtccgagatcagcaggggaacgtactcttatctcctgaagaggttagtgaaacacagggaacag +agaagttgacaataacatattcatcctcaatgatgtgggaaatcaacggtcctgagtcagtgcttgttaacacttatcaa +tggatcatcaggaattgggagactgtaaagattcaatggtctcaagatcccacaatgctgtacaataagatggagtttga +atcgttccaatccttggtgccaaaggctgccagaagccaatatagtggatttgtgagaacactattccaacagatgcgtg +atgttttggggacatttgatactgtccaaataatcaagctgctaccatttgcagcagccccaccggagccgagcagaatg +cagttttcttctctaactgtgaatgtgagaggctcaggaatgagaatactcgtgaggggtaactcccccgtgttcaacta +caacaaggcaaccaaaaggcttacagtcctcggaaaggacgcaggtgcattaacagaagatccagacgagggaacagccg +gggtggaatctgcagtattgaggggattcctaattctaggcagagaggacaaaagatatggacccgcattgagcatcaat +gaactgagcaatcttgcaaaaggggagaaggctaatgtattgataatgcaaggagacgtggtgttggtaatgaaacggaa +acgggactttagcatacttactgacagccagacagcgaccaaaagaattcggatggccatcaattagtgttgaatagttt +aaaaacgaccttgtttctact \ No newline at end of file diff --git a/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/2.fa b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/2.fa new file mode 100644 index 00000000..9ecbc997 --- /dev/null +++ b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/2.fa @@ -0,0 +1,31 @@ +>5781|A/Goose/Guangdong/1/96|EPI_ISL_1254|PB1|| +agcaaaagcaggcaaaccatttgaatggatgtcaatccgactttacttttcttaaaagtgccagcgcaaaatgctataag +taccacattcccttatactggagatcctccatacagccatggaacaggaacaggatacaccatggacacagtcaacagaa +cacatcaatattcagaaaaggggaaatggacaacgaacacagagactggagcaccccaactcaatccgattgatggacca +ctacctgaggataatgagccgagtgggtatgcacaaacagattgtgtattggaagcaatggctttccttgaagaatccca +cccagggatctttgaaaactcgtgtcttgaaacgatggaagttgttcagcaaacaagagtggataagctgacccaaggtc +gccaaacctatgactggacattgaaaagaaaccagccggctgcaaccgctttggccaacactatagaggtcttcagatcg +aatggtctaacagccaatgaatcgggaaggctaatagatttcctcaaagacgtgatggaatcaatggataagggagaaat +ggaaataataacacatttccagagaaagagaagagtgagggacaacatgaccaagaaaatggtcacacaaagaacaatag +ggaagaaaaaacaaaggctgaacaaaaggagctacctaataagagcactgacactgaacacaatgacaaaagacgcagaa +agaggcaaattgaagaggcgggcaattgcaacacccgggatgcaaatcagaggattcgtgtactttgtcgaaacactagc +gaggagtatctgtgagaaacttgagcaatctggactccccgtcggagggaatgaaaagaaggctaaattggcaaatgtcg +tgaggaagatgatgactaactcacaagatacagagctctcttttacaattactggagacaacaccaaatggaatgagaat +cagaaccctcggatgtttctagcaatgataacatacatcacaaggaaccaacctgaatggtttagaaatgtcttaagcat +tgctcctataatgttctcaaacaagatggcaagattagggaaaggatacatgttcgaaagtaagagcatgaagctacgga +cacaaataccagcagaaatgcttgcaagcattgacttgaaatacttcaacgaatcaacgagaaagaaaatcgagaaaata +agacctctactaatagatggcacagcctcattgagtcctggaatgatgatgggcatgttcaatatgctgagtacagtctt +aggagtttcaatcctgaatcttgggcagaagaggtacaccaaaaccacatactggtgggacggactccaatcctctgatg +atttcgctctcatagtgaatgcaccaaatcatgagggaatagaagcaggggtggataggttctataggacttgcaaacta +gttggaatcaatatgaccaagaagaagtcttacataaatcggacaggaacatgtgaattcacaagcttcttctaccgcta +tgggttcgtagccaacttcagtatggagctgcccagctttggagtgtctgggattaatgaatcggctgacatgagcattg +gtgttacagtgataaagaacaatatgatggacaacgaccttggaccagcaacagctcagatggctcttcagctattcatt +aaggactacagatacccataccgatgccacaggggggatacacaaatccaaacgaggagatcattcgagctgaagaagct +gtgggagcagacccgctcaaaggcaggactgttggtttcagatggaggaccaaacccatacaatatccggaatctccaca +ttccggaggctggcttgaagtgggaattgatggatgaagactaccagggcagactgtgtaatcctctgaacccgtttgtt +agtcataaggaaattgagtctgtcaacaatgctgtggtaatgccagctcatggcccagccaagagcatggaatatgatgc +agttgcgactacacattcatggattcccaagaggaatcgttccattctcaacaccagccaaagggggattcttgaggatg +aacagatgtatcagaagtgctgcaatctattcgagaaattcttccctagcagttcatatcggaggccagttggaatttcc +agcatggtggaggccatggtgtctagggcccgaattgatgcacgaattgacttcgagtctggaaggattaagaaagaaga +gtttgctgagatcatgaagatctgttccaccattgaagagctcggacggcaaaaatagtgaatttagcttgtccttcatg +aaaaaatgccttgtttctact \ No newline at end of file diff --git a/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/3.fa b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/3.fa new file mode 100644 index 00000000..091cc5eb --- /dev/null +++ b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/3.fa @@ -0,0 +1,29 @@ +>5783|A/Goose/Guangdong/1/96|EPI_ISL_1254|PA|| +agcaaaagcaggtactgatccaaaatggaagactttgtgcgacaatgcttcaatccaatgattgtcgagcttgcggaaaa +ggcaatgaaagaatatggggaagatccgaaaatcgaaacgaacaaatttgccgcaatatgcacgcacttagaagtctgtt +tcatgtattcagatttccactttattgatgaacggggcgaatcaacaattatagaatctggcgatcccaatgcattattg +aaacaccggtttgaaataatcgaagggagggaccgaacaatggcctggacagtggtgaatagtatctgcaacaccacagg +agttgagaagcctaaatttctcccagatttgtatgactacaaggagaaccgatttattgaaattggagtgacacggaggg +aagttcacacatactatctagaaaaagccaacaagataaaatctgagaagacacacattcacatattctcattcactgga +gaggaaatggccaccaaagcggactacacccttgatgaagaaagcagggcccgaatcaaaaccaggctgttcactataag +gcaggaaatggccagtaggggtttatgggattcctttcgtcagtccgagagaggcgaagagacagttgaagaaagatttg +aaatcacagggactatgtgcaggcttgccgaccaaagtctcccacctaatttctccagccttgaaaaatttagagcctat +gtggatggattcgaaccgaacggctgcattgagggcaagctttctcaaatgtcgaaagaagtaaacgccagaattgagcc +atttctgaagacaacaccacgccctcttagattacctgatgggcctccctgctctcagcggtcgaagtttttgctgatgg +atgcccttaaattaagcatcgaagacccgagtcatgagggggaggggataccgctatatgatgcaatcaaatgcatgaaa +acatttttcggctggaaagagcccaacattgtaaaaccacatgaaaaaggcataaaccccaattacctcctggcttggaa +gcaggtgctggcagagctccaagatattgaaaacgaggagaaaattccaaagacaaagaacatgaggaaaacaagccaat +tgaagtgggcacttggtgagaatatggcaccagagaaagtagactttgaggattgcaaagatgttagcgatctaaggcag +tatgacagtgatgaaccaaagcctagatcactagcaagctggatccagagtgaattcaacaaggcatgcgaattgacaga +ttcaagttggattgaacttgatgaaataggggaagacgttgctccaattgagcacattgcaagtatgagaaggaactatt +tcacagcggaagtatcccattgcagggctactgaatacataatgaagggagtgtacataaacacagctttgttgaatgca +tcctgtgcagccatggatgacttccaactgatcccaatgataagcaaatgcagaaccaaagaaggaagacggaaaactaa +cctgtatggattccttataaaaggaagatcccatttgagaaatgacaccgatgtggtaaactttgtgagtatggaattct +ctcttactgatccgaggctggagccacacagatgggaaaagtactgcgttcttcggataggagacatgctcttacggact +gaaataggccaagtgtcaaggcccatgtttctttatgtgagaaccaatggaacctccaagatcaagatgaaatggggcat +ggaaatgaggcgatgcccttttcaatcccttcaacagattgagagcatgattgaggccgagtcttctgtcaaagaaaaag +acatgactaaagaattctttgaaaacaaatcagaaacatggccaattggagaatcacccaagggagtggaggaaggctcc +atcgggaaggtgtgcagaaccttactggctaaatctgttttcaacagtctatatgcatctccacaactcgaggggttttc +agctgaatcaagaaaattgcttctcattgttcaggcacttagggacaacctggaacctggaaccttcgatcttggggggc +tatatgaagcaattgaggagtgcctgattaatgatccctgggttttgcttaatgcatcttggttcaactccttcctcaca +catgcactaagatagttgtggcaatgctactatttgctatccatactgtccaaaaaagtaccttgtttctact \ No newline at end of file diff --git a/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/4.fa b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/4.fa new file mode 100644 index 00000000..ecaf1692 --- /dev/null +++ b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/4.fa @@ -0,0 +1,23 @@ +>5789|A/Goose/Guangdong/1/96|EPI_ISL_1254|HA|| +gcaggggtataatctgtcaaaatggagaaaatagtgcttcttcttgcaatagtcagtcttgtcaaaagtgatcagatttg +cattggttaccatgcaaacaactcgacagagcaggttgacacaataatggaaaagaacgttactgttacacatgcccaag +acatactggaaaagacacacaatgggaagctctgcgatctaaatggagtgaagcctctcattttgagagattgtagtgta +gctggatggctcctcggaaaccctatgtgtgacgaattcatcaatgtgccggaatggtcttacatagtggagaaggccag +tccagccaatgacctctgttacccaggggatttcaacgactatgaagaactgaaacacctattgagcagaacaaaccatt +ttgagaaaattcagatcatccccaaaagttcttggtccaatcatgatgcctcatcaggggtgagctcagcatgtccatac +catgggaggtcctcctttttcagaaatgtggtatggcttatcaaaaagaacagtgcatacccaacaataaagaggagcta +caataataccaaccaagaagatcttttagtactgtgggggattcaccatcctaatgatgcggcagagcagacaaagctct +atcaaaacccaaccacttacatttccgttggaacatcaacactgaaccagagattggttccagaaatagctactagaccc +aaagtaaacgggcaaagtggaagaatggagttcttctggacaattttaaagccgaatgatgccatcaatttcgagagtaa +tggaaatttcattgctccagaatatgcatacaaaattgtcaagaaaggggactcagcaattatgaaaagtgaattggaat +atggtaactgcaacaccaagtgtcaaactccaatgggggcgataaactctagtatgccattccacaacatacaccccctc +accatcggggaatgccccaaatatgtgaaatcaaacagattagtccttgcgactggactcagaaatacccctcagagaga +gagaagaagaaaaaagagaggactatttggagctatagcaggttttatagagggaggatggcagggaatggtagatggtt +ggtatgggtaccaccatagcaatgagcaggggagtggatacgctgcagacaaagaatccactcaaaaggcaatagatgga +gtcaccaataaggtcaactcgatcattgacaaaatgaacactcagtttgaggccgttggaagggaatttaataacttgga +aaggaggatagagaatttaaacaagcagatggaagacggattcctagatgtctggacttataatgctgaacttctggttc +tcatggaaaatgagagaactctagactttcatgactcaaatgtcaagaacctttatgacaaggtccgactacagcttagg +gataatgcaaaggagctgggtaatggttgtttcgagttctatcacaaatgtgataatgaatgtatggaaagtgtaaaaaa +cggaacgtatgactacccgcagtattcagaagaagcaagactaaacagagaggaaataagtggagtaaaattggaatcaa +tgggaacttaccaaatactgtcaatttattcaacagtggcgagttccctagcactggcaatcatggtagctggtctatct +ttatggatgtgctccaatggatcgttacaatgcagaatttgcatttaaatttgtgagttcagattgtagttaaaaacacc \ No newline at end of file diff --git a/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/5.fa b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/5.fa new file mode 100644 index 00000000..d062a900 --- /dev/null +++ b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/5.fa @@ -0,0 +1,21 @@ +>5785|A/Goose/Guangdong/1/96|EPI_ISL_1254|NP|| +agcaaaagcagggtagataatcactcactgagtgacatcaacatcatggcgtctcagggcaccaaacgatcttatgaaca +gatggaaactggtggagaacgccagaatgctactgagatcagagcatctgttggaagaatggttggtggaattgggaggt +tttatatacagatgtgcactgaactcaaactcagcgactatgaaggaaggctgattcagaacagcataacaatagagaga +atggttctctctgcatttgatgaaaggaggaacaaatacctggaagaacatcccagtgcggggaaggacccaaagaaaac +tggaggtccaatctaccgaagaagagacggaaaatgggtgagagagctgattctgtatgacaaagaggagatcaggagaa +tttggcgtcaagcgaacaatggagaagatgcaactgctggtctcactcacatgatgatctggcattccaatctaaatgat +gccacataccagagaacaagagctctcgtgcgtactgggatggaccctagaatgtgctctctgatgcaaggatcaactct +cccgaggagatctggagctgctggtgcggcagtaaagggagtcggaacgatggtgatggaactaattcggatgataaagc +gagggattaacgatcggaatttctggagaggtgaaaatgggcgaagaacaagaattgcatatgagagaatgtgcaacatc +ctcaaagggaaattccaaacagcagcacaaagagcaatgatggatcaggtacgggaaagcagaaatcctgggaatgctga +gattgaagatctcatatttctggcacggtctgcactcatcctgagaggatcagtggcccacaagtcctgcttgcctgctt +gtgtgtacgggcttgccgtggccagtggatatgactttgagagagaagggtactctctggtcgggattgatcctttccgt +ctgctgcaaaacagccaggtctttagtctaattagaccaaatgagaatccagcacataaaagtcaattggtgtggatggc +atgccattctgcagcatttgaagatctgagagtctcaagcttcatcagagggacaagagtggccccaaggggacaactat +ctactagaggagttcaaattgcttcaaatgagaacatggaaacaatggactccagcactcttgaactgagaagcagatat +tgggctataaggaccaggagtggaggaaacaccaaccagcagagagcatctgcaggacaaatcagtgtgcagcctacttt +ctcggtacagagaaatcttcccttcgaaagagcgaccattatggcggcattcacagggaatacagagggcagaacatctg +acatgaggactgaaatcataaggatgatggaaagctccagaccagaagatgtgtctttccaggggcggggagtcttcgag +ctctcggacgaaaaggcaacgaacccgatcgtgccttcctttgacatgagtaatgaaggatcttatttcttcggagacaa +tgcagaggaatatgacaattgaagaaaaatacccttgtttctact \ No newline at end of file diff --git a/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/6.fa b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/6.fa new file mode 100644 index 00000000..9984eb32 --- /dev/null +++ b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/6.fa @@ -0,0 +1,20 @@ +>5787|A/Goose/Guangdong/1/96|EPI_ISL_1254|NA|| +agcaaaagcaggagattaaaatgaatccaaatcagaagataataaccattggatcaatctgtatggtagttgggataatt +agcttgatgttacaaattgggaacataatctcaatatgggtcagtcattcaattcagacagggaatcaacaccaagctga +accatgcaatcaaagcattattacttatgaaaacaacacctgggtaaatcaaacatatgtcaacatcagcaataccaatt +ttcttactgaaaaagctgtggcttcagtaacattagcgggcaattcatctctttgccccattagcggatgggctgtacac +agtaaggacaacggtataagaatcggttccaagggggatgtgtttgttataagagagccgttcatctcatgctcccactt +ggaatgcagaactttctttttgactcagggagccttgctgaatgacaagcactccaatgggaccgtcaaagacagaagcc +ctcacagaacattgatgagttgtcctgtgggtgaggctccctccccatataactcaaggtttgagtctgttgcttggtcg +gcaagtgcttgccatgatggcaccagttggttgacaattggaatttctggcccagacaatggggctgtggctgtattgaa +atacaacggcataataacagacactatcaagagttggaggaacaacatactgagaactcaagagtctgaatgtgcatgtg +taaatggctcttgctttactgtaatgactgacggaccaagtaatgggcaggcctcatataagatcttcaaaatggaaaaa +gggaaagtagttaaatcagtcgaattgaatgcccctaattatcactatgaggagtgctcctgttatcctgatgctggcga +aatcacatgtgtgtgcagggataattggcatggctcaaatcggccatgggtatctttcaatcaaaatttggagtatcaaa +taggatatatatgcagtggagttttcggagacaatccacgccccaatgatggaacaggcagttgtggtccggtgtcccct +aacggggcatatggagtaaaagggttttcatttaaatacggcaatggtgtttggatcgggagaaccaaaagcactaattc +caggagcggctttgaaatgatttgggatccaaatgggtggactggaacggacagtagcttctcggtgaaacaagatatcg +tagcaataactgattggtcaggatatagcgggagttttgtccagcatccagaactgacaggattagattgcataagacct +tgtttctgggttgagctaatcagagggcggcccaaagagagcacaatttggactagtgggagcagcatatctttttgtgg +tgtaaatagtgacactgtgggttggtcttggccagacgatgccgagttgccattcaccattgacaagtagtttgttcaaa +aaactccttgtttctact \ No newline at end of file diff --git a/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/7.fa b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/7.fa new file mode 100644 index 00000000..2613c3dd --- /dev/null +++ b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/7.fa @@ -0,0 +1,14 @@ +>5791|A/Goose/Guangdong/1/96|EPI_ISL_1254|MP|| +agcaaaagcaggtagatattgaaaaatgagtcttctaaccgaggtcgaaacgtacgttctctctatcgtcccgtcaggcc +ccctcaaagccgagatcgcgcagagacttgaggatgtctttgcaggaaagaacaccgatctcgaggctctcatggaatgg +ctaaagacaagaccaatcctgtcacctctgactaaagggattttaggatttgtgttcacgctcaccgtgcccagtgagcg +aggactgcagcgtagacgctttgtccagaatgccttaaatggaaatggagatccaaacaatatggatagggcagttaagc +tatacaagaagctgaaaagagaaataacattccatggggctaaggaggtcgcactcagctactcaaccggtgcacttgcc +agttgtatgggtctcatatacaacaggatgggaacggtgaccacagaagtggcttttggcctagtgtgtgccacttgtga +gcagattgcagattcacagcatcggtctcacagacagatggcaactaccaccaacccactaatcaggcatgagaacagaa +tggtgctggccagcactacagctaaggctatggagcagatggctggatcgagtgagcaggcagcggaagccatggaggtt +gctagtcaggctaggcagatggtgcaggcaatgaggacaattgggactcatcctagctccagtgccggtctgaaagataa +tcttcttgaaaatttgcaggcctaccaaaaacgaatgggagtgcaaatgcagcgattcaagtgatcctcttgttgttgcc +gcaagtatcattgggatactgcacttgatattgtggattcttgatcgtcttttcttcaaatgcatttatcgtcgccttaa +atacggtttgaaaagagggccttctacggaaggggtacctgagtctatgagggaagagtatcggcaggaacagcagagtg +ctgtggatgttgacgatggtcattttgtcaacatagagctggagtaaaaaactaccttgtttctact \ No newline at end of file diff --git a/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/8.fa b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/8.fa new file mode 100644 index 00000000..03582dd2 --- /dev/null +++ b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/8.fa @@ -0,0 +1,12 @@ +>5794|A/Goose/Guangdong/1/96|EPI_ISL_1254|NS|| +gtgacaaagacataatggattccaacacgataacctcgtttcaggtagattgttatctatggcacataagaaagctactc +agtatgagagacatgtgtgatgccccctttgatgacaggctccgaagagaccaaaaggcattaaagggaagaggcagcac +acttggactcgatttaagagtggctacaatggaggggaaaaagatcgttgaggacatcctgaagagtgagacaaatgaaa +acctcaaaatagccattgcttccagtcctgctcctcggtatatcaccgatatgagcatagaggagatgagccgagaatgg +tacatgctgatgcctaggcagaaaataactggaggccttatggtgaaaatggaccaagccataatggataaaagaattat +ccttaaagcaaatttctcagttctatttgatcaactagagacattagtctctctgagggcattcacagaaagtggtgcta +ttgtggctgaaatatttcccattccctccgtaccaggacattttacagaggatgtcaaaaatgcaattggaatcctcatc +ggtggacttgaatggaatgataactcaattcgagcgtctgaaaatatacagagattcgcttggggaatccatgatgagaa +tgggggaccttcactccctccaaaacagaaacgctacatggcgaaacgagttgagtcagaagtttgaagagatcagatgg +ctcattgctgaatgtagaaatatactgacaaagactgaaaatagctttgaacagataacatttttgcaagcattgcaact +cttacttgaagttgagagtgagataaggaccttctcttttcagcttatttaatactaaaaaacac \ No newline at end of file diff --git a/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/DESCRIPTION b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/DESCRIPTION new file mode 100644 index 00000000..b1cf7d1b --- /dev/null +++ b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/DESCRIPTION @@ -0,0 +1 @@ +A/Goose/Guangdong/1/96 EPI_ISL_1254 \ No newline at end of file diff --git a/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/NOTES b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/NOTES new file mode 100644 index 00000000..c80567eb --- /dev/null +++ b/static_data/flu/mut_references/H5NX/A-Goose-Guangdong-1-96/NOTES @@ -0,0 +1,29 @@ +See: https://apps.who.int/iris/bitstream/handle/10665/366577/WER9812-111-125.pdf + +GISAID entry: + +|-----------|---------------------------|-----------|---------------|---------------| +| segment | identifier | length | accession # | INSDC | +|-----------|---------------------------|-----------|---------------|---------------| +| PB2 | A/Goose/Guangdong/1/96 | 2341 | EPI5779 | AF144300 | +| PB1 | A/Goose/Guangdong/1/96 | 2341 | EPI5781 | AF144301 | +| PA | A/Goose/Guangdong/1/96 | 2233 | EPI5783 | AF144302 | +| HA | A/Goose/Guangdong/1/96 | 1760 | EPI5789 | AF144305 | +| HA | A/Goose/Guangdong/1/96 | 1707 | EPI5797 | AF148678 | +| NP | A/Goose/Guangdong/1/96 | 1565 | EPI5785 | AF144303 | +| NA | A/Goose/Guangdong/1/96 | 1458 | EPI5787 | AF144304 | +| MP | A/Goose/Guangdong/1/96 | 1027 | EPI5791 | AF144306 | +| NS | A/Goose/Guangdong/1/96 | 865 | EPI5794 | AF144307 | +|-----------|---------------------------|-----------|---------------|---------------| + +Features from: +Taxid 93838 on NCBI Virus: + +NC_007361 NA +NC_007357 PB2 +NC_007358 PB1, PB1-F2 +NC_007359 PA, PA-X +NC_007360 NP +NC_007362 HA +NC_007363 MP (7) +NC_007364 NS (8) \ No newline at end of file diff --git a/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/1.fa b/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/1.fa new file mode 100644 index 00000000..e4885d0e --- /dev/null +++ b/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/1.fa @@ -0,0 +1,30 @@ +>568646|A/Shanghai/02/2013|EPI_ISL_173625|PB2|passage_details:_E1| +atggaaagaataaaagaactaagagatttgatgtcacagtctcgcactcgcgagatactgacaaaaacaactgtggacca +tatggccataatcaagaaatatacatcaggaagacaggagaagaatcctgcccttaggatgaagtggatgatggcaatga +aatatccaattacggcagacaaaaggataatggagatgatcccggaaagaaatgagcaaggtcagaccctttggagcaag +acaaatgatgctggatcagacagagtgatggtgtcacctctggctgtgacgtggtggaacagaaatggaccaacgacaag +cacagtccattatccaaaggtctataaaacctattttgaaaaggtcgaaaggctaaaacatggaaccttcggccccgttc +acttcagaaaccaggttaaaatacgccgcagggtcgacataaacccgggccatgcagatcttagtgctaaagaagcacag +gatgtcatcatggaggtcgtattcccaaacgaagttggagccagaatattgacatcagagtcacagttaacgattaccaa +ggaaaagaagaaggagcttcaggactgcaaaattgcccctttaatggtggcttacatgttggagagagaactggttcgca +aaacaagattcctaccagtagctggagggacaagcagcgtgtatatcgaggtgttgcatttgacccaagggacctgctgg +gagcaaatgtacacaccgggaggggaagtgagaaatgatgatgttgatcagagtttaattattgctgctagaaatattgt +tagaagagcaacagtatcagcagacccgttggcttcgcttttggagatgtgccatagtacacagattggcgggattagga +tggttgacatccttagacaaaacccaacagaagaacaggctgtggatatatgtaaggcagcaatgggtctaaggatcagt +tcatccttcagctttggaggtttcactttcaaaaggacaagtgggtcatctgtcaaaagggaagaagaagtgctcacagg +caacctccaaacattgaaaataagagtacatgaaggatatgaggaattcacaatggtcgggcgaagagcaacagccattc +taaggaaagcaaccagaagactgatccaactgatagtgagtgggaaagacgagcaatcaatcgccgaggcaatcatagtg +gcaatggtattctcacaagaggattgtatgataaaggcagtgagaggtgatttgaactttgtcaacagagcaaaccagcg +gctaaatcccatgcatcaactcctgaggcatttccaaaaggatgcaaaggtcctgtttcaaaactggggaattgaaccca +ttgacaatgtaatggggatgatcggaatattgcctgacatgacccccagcacagagatgtcattgagaggagtgagagtt +agtaaaatgggagtagatgaatattccagcactgagagagtggtcgtgagtattgatcgtttcttgagggtccgagacca +gaggggaaacgtactcctgtctcctgaagaggttagtgaaacacagggaacagaaaagctgactataacatattcatcgt +ccatgatgtgggagatcaatggtccggaatcagtgctagttaacacatatcaatggatcattagaaattgggaaaatgta +aagattcaatggtcccaagatcctacaatgctatacaataagatggaatttgaaccctttcaatccctagtgcctaaagc +tgccaggggccaatatagtgggttcgtgagggttctattccaacagatgcgtgacgtactgggaacatttgacactgtcc +aaataataaagctattaccatttgcagcagccccgccgaagcagagtaggatgcagttctcttctctaactgtgaatgtg 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+gggtatgcacaaacggattgtgtattggaagcaatggctttccttgaagaatctcacccagggatctttgaaaactcgtg +tctcgaaacgatggaaattgttcagcaaacaagagtggataaactgacccaaggccgccagacctatgactggacgttga +atagaaatcagccggctgctaccgcattggccaacactatagaggtattcagatcgaatggcctgacagccaatgaatca +ggaaggttgatcgatttcctcaaggacgtgatggattcaatggataaggaagaaatggagattacaacacatttccagag +gaagaggagagtgagggacaacatgaccaagaaaatggtcacacagagaacaataggaaagaaaaaacaaagactgaaca +aaaggagctacctaataagagcacttacattgaacacaatgacaaaggatgctgaaagaggcaagctgaaaaggagggca +atcgcaacacccgggatgcaaatcagaggattcgtgtattttgtagaagcactagcgaggagcatctgtgagaaacttga +gcaatctggcctccctgtcggagggaatgagaagaaagctaaattggcaaatgttgtgaggaagatgatgactaattcac +aagatacagagctctccttcacaattactggggacaacaccaaatggaatgagaatcaaaacccccggatgtttctagca +atgataacatacatcacaagaaaccagccagaatggtttagaaatgtcttaagcattgctcctataatgttctcaaacaa +gatggcgagattaggaaaagggtacatgttcgaaagtaagagtatgaagttacggacacaagtaccagcggaaatgctcg +caaatattgacctgaaatacttcaacaaatcaacaagagagaaaatcgagaaaataagacctctactgatagatggcaca +gcctcattgagtcctggaatgatgatgggcatgttcaacatgttgagtacagtcttaggagtttcaattctgaatctcgg +gcagaagaagtacaccaaaaccacatattggtgggacggactccaatcctcagatgacttcgccctcatagtgaatgcac +cgaatcatgagggaatacaggcaggagtagataggttctatagaacctgcaaattagttgggataaacatgagcaagaag +aaatcctacataaatcggacaggaacattcgaattcacaagctttttctaccgctatggattcgtagctaacttcagtat +ggagttgcccagttttggagtgtccgggattaatgagtcagctgacatgagcgttggtgttacagtaataaagaacaata +tgataaacaacgatcttggaccagcaacagcccaaatggcccttcagctatttatcaaagactacagatacacataccga +tgtcacaggggtgatacgcaaattcaaacgaggagagcattcgagctgaagaagctgtgggagcagacccgttcgaaggc +aggactgttggtttcagatggagggccaaacctgtacaatatccggaacctccacattccagaggtctgcttgaaatggg +aattgatggatgaagactaccaaggcaggttgtgtaatcctatgaacccgtttgtcagtcataaggaaattgattcagtc +aacaatgctgtggtgatgccagctcatggcccagccaaaagcatggagtatgatgccgttgcaaccacacattcatggat +tcctaagaggaatcgctccattctcaacaccagccaaagggggattcttgaggacgaacagatgtaccagaagtgctgca +acctattcgaaaagttcttccccagcagttcgtacaggaggccagttggaatttccagcatggtggaggccatggtgtct +agggcccgaattgatgcacgaattgacttcgaatctggaaggattaagaaagaagagtttgctgagatcatgaagatctg +ttccaccattgaagagctcagacggcaaaaatagtgaatttagcttgtccttcatga \ No newline at end of file diff --git a/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/3.fa b/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/3.fa new file mode 100644 index 00000000..608cc66e --- /dev/null +++ b/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/3.fa @@ -0,0 +1,29 @@ +>596649|A/Shanghai/02/2013|EPI_ISL_173625|PA|passage_details:_E1| +atggaagactttgtgcgacagtgcttcaatccaatgatcgtcgagcttgcggaaaaggcaatgaaagaatatggggaaga +tccgaaaatcgaaacaaacaaattcgcatcaatatgcacacacttagaagtctgcttcatgtactctgatttccacttca +tcgacgaacgaggcgaatcaactataatagaatctggcgatccaaatgcgctgctgaaacaccgatttgaaataatcgaa +gggagagaccgaacaatggcctggacagtggtgaatagtatctgcaacaccacaggagccgaaaaacccaaatttctccc +ggatctgtatgactacaaggaaaaccgtttcattgaaattggagtgacgaggagggaagtccacatatattacctagaga +aagccaataaaataaaatccgagaagacacacatccatattttttcattcactggagaagagatggccaccaaagcagat +tacactcttgacgaagaaagcagggcaagaatcaaaaccaggctgttcaccataaggcaggaaatggccagcaggggtct +atgggattcctttcgtcagtctgaaagaggcgaagaaacaattgaagaaagatttgaaatcacaggaaccatgcgcaggc +ttgccgaccaaagtctcccaccgaacttctccagccttgaaaactttagagcctatgtggatggattcgaaccgaacggc +tgcattgagggcaagctttctcagatgtcaaaagaagtgaacgccagaattgagccatttctaagaacaacaccacgccc +tctcagattgcctaatgggcctccctgctctcagcggtcgaaattcttgctgatggatgctctgaaattaagcattgagg +acccgagccacgaaggggaggggataccgctatatgatgcgatcaaatgcatgaaaacgttcttcgggtggaaagagccc +aacattatcaaaccacatgagaaaggcataaaccccaattatctcctgacttggaagcaggtgctagcagaacttcagga +cattgaaaatgaagagaagattccaaggacaaagaacatgaagaaaacaagccaattaaagtgggcactcggtgagaaca +tggcaccggagaaggtggactttgaggattgcaaagatgtcaacgacttgaaacagtacaacagtgatgagccagagccc +agatcactagcatgttggatccagaatgaattcaacaaggcgtgtgaactgactgactcaagctgggtagaacttgatga +aataggggaagatgttgccccaatcgaacacattgcaagcatgagacggaactattttacagcagaggtgtcccactgca 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new file mode 100644 index 00000000..a61634c8 --- /dev/null +++ b/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/4.fa @@ -0,0 +1,23 @@ +>568648|A/Shanghai/02/2013|EPI_ISL_173625|HA|passage_details:_E1| +atgaacactcaaatcctggtattcgctctgattgcgatcattccaacaaatgcagacaaaatctgcctcggacatcatgc +cgtgtcaaacggaaccaaagtaaacacattaactgaaagaggagtggaagtcgtcaatgcaactgaaacagtggaacgaa +caaacatccccaggatctgctcaaaagggaaaaggacagttgacctcggtcaatgtggactcctggggacaatcactgga +ccacctcaatgtgaccaattcctagaattttcagccgatttaattattgagaggcgagaaggaagtgatgtctgttatcc +tgggaaattcgtgaatgaagaagctctgaggcaaattctcagagaatcaggcggaattgacaaggaagcaatgggattca +catacagtggaataagaactaatggagcaaccagtgcatgtaggagatcaggatcttcattctatgcagaaatgaaatgg +ctcctgtcaaacacagataatgctgcattcccgcagatgactaagtcatataaaaatacaagaaaaagcccagctctaat +agtatgggggatccatcattccgtatcaactgcagagcaaaccaagctatatgggagtggaaacaaactggtgacagttg +ggagttctaattatcaacaatcttttgtaccgagtccaggagcgagaccacaagttaatggtctatctggaagaattgac 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+taagtttggaaaaaacacccttgtttct \ No newline at end of file diff --git a/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/5.fa b/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/5.fa new file mode 100644 index 00000000..0c1ee37c --- /dev/null +++ b/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/5.fa @@ -0,0 +1,20 @@ +>568649|A/Shanghai/02/2013|EPI_ISL_173625|NP|passage_details:_E1| +atggcgtctcaaggcaccaaacgatcctatgaacagatggaaactggtggggaacgccagaatgctactgagatcagggc +atctgttggaagaatggttagcggcattgggagattctacatacagatgtgtacagaactcaaactcagtgacaatgaag +ggaggctgattcagaacagtataacaatagagagaatggtactctctgcatttgatgaaagaaggaacagatacctggaa +gagcaccccagtgcaggaaaggaccctaagaaaactggaggtccaatttacaggagaagagacggaaaatgggtgagaga +gctgatcctgtatgacaaagaggaaatcaggagaatttggcgacaagcgaacaatggagaggatgcaactgctggtctta +cccatctgatgatatggcattccaacctgaatgatgctacctatcagagaacgagagctctcgtgcgtactggaatggat +ccccggatgtgctctctgatgcaaggatcaactctcccgaggagatctggagctgcaggtgcagcagtgaaggggatagg 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diff --git a/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/6.fa b/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/6.fa new file mode 100644 index 00000000..3aea21bf --- /dev/null +++ b/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/6.fa @@ -0,0 +1,19 @@ +>568652|A/Shanghai/02/2013|EPI_ISL_173625|NA|passage_details:_E1| +atgaatccaaatcagaagattctatgcacttcagccactgctatcataataggcgcaatcgcagtactcattggaatggc +aaacctaggattgaacataggactgcatctaaaaccgggctgcaattgctcacactcacaacctgaaacaaccaacacaa +gccaaacaataataaacaactattataatgaaacaaacatcaccaayatccaaatggaagagagaacaagcaggaatttc +aataacttaactaaagggctctgtactataaattcatggcacatatatgggaaagacaatgcagtaagaattggagagag +ctcggatgttttagtcacaagagaaccctatgtttcatgcgacccagatgaatgcaggttctatgctctcagccaaggaa +caacaatcagagggaaacactcaaacggaacaatacacgataggtcccagtatcgcgccctgataagctggccactatca +tcaccgcccacagtgtacaacagcagggtggaatgcattgggtggtcaagtactagttgccatgatggcaaatccaggat +gtcaatatgtatatcaggaccaaacaacaatgcatctgcagtagtatggtacaacagaaggcctgttgcagaaattaaca +catgggcccgaaacatactaagaacacaggaatctgaatgtgtatgccacaacggcgtatgcccagtagtgttcaccgat +gggtctgccactggacctgcagacacaagaatatactattttaaagaggggaaaatattgaaatgggagtctctgactgg +aactgctaagcatattgaagaatgctcatgttacggggaacgaacaggaattacctgcacatgcagggacaattggcagg +gctcaaatagaccagtgattcagatagacccagtagcaatgacacacactagtcaatatatatgcagtcctgttcttaca +gacaatccccgaccgaatgacccaaatataggtaagtgtaatgacccttatccaggtaataataacaatggagtcaaggg +attctcatacctggatggggctaacacttggctagggaggacaataagcacagcctcgaggtctggatacgagatgttaa +aagtgccaaatgcattgacagatgatagatcaaagcccattcaaggtcagacaattgtattaaacgctgactggagtggt +tacagtggatctttcatggactattgggctgaaggggactgctatcgagcgtgtttttatgtggagttgatacgtggaag +acccaaggaggataaagtgtggtggaccagcaatagtatagtatcgatgtgttccagtacagaattcctgggacaatgga +actggcctgatggggctaaaatagagtacttcctctaa \ No newline at end of file diff --git a/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/7.fa b/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/7.fa new file mode 100644 index 00000000..9fbff540 --- /dev/null +++ b/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/7.fa @@ -0,0 +1,14 @@ +>568650|A/Shanghai/02/2013|EPI_ISL_173625|MP|passage_details:_E1| +atgagtcttctaaccgaggtcgaaacgtacgttctctctatcattccatcaggccccctcaaagccgagatcgcacagag +acttgaggatgtttttgcagggaagaacgcagatctcgaggctctcatggagtggataaagacaagaccaatcctgtcac +ctctgactaaggggattttagggtttgtgttcacgctcaccgtgcccagtgagcgaggactgcagcgtagacggtttgtc +caaaacgccctaaatgggaatggagacccaaacaacatggacaaggcggttaaattatacaagaaactgaagagggaaat +gacatttcatggagcaaaggaagttgcactcagttactcaactggtgcgcttgccagctgcatgggtctcatatacaaca +gaatggggactgtgaccgcagaaggggctcttggactagtatgtgccacttgtgagcagattgctgacgcacaacatcgg +tcccacaggcagatggcgactactactaacccactaattaggcatgagaatagaatggtactagccagcactacggctaa +ggctatggagcagatggctggatcaagtgaacaggcagcggaagccatggaagttgcaagtcaggctaggcaaatggtgc +aggctatgagaacagttgggactcaccctaactccagtacaggtctaaaagatgatcttattgaaaatttgcaggcctac +cagaaccggatgggagtgcaactgcagcggttcaagtgagcctctagtcgttgcagctaacattattgggatattgcact +tgatattgtggattcttgatcgtcttttcttcaaatgcatttatcgtcgttttaaatacggtttgaaaagagggccttct +acggaaggaatgcctgagtctatgagggaagaatatcggcaggaacagcagaatgctgtggatgttgacgatggtcattt +tgtcaacatagagctgaagtaaaaa \ No newline at end of file diff --git a/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/8.fa b/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/8.fa new file mode 100644 index 00000000..f5ef724d --- /dev/null +++ b/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/8.fa @@ -0,0 +1,12 @@ +>568651|A/Shanghai/02/2013|EPI_ISL_173625|NS|passage_details:_E1| +atggattccaatactgtgtcaagcttccaggtagactgctttctttggcatgtccgcaaacgatttgcagaccaagaaat +gggtgatgccccatttctagaccggcttcgccgagatcagaagtccctgagaggaagaagcagcactcttggtctggaca +tcagaactgccacgcgtgaaggaaagcatatagtggagcggattttagaggaagagtcagatgaagcatttaaaatgagt +attgcttcagtgccagctccacgctatctaactgacatgactcttgaagaaatgtcaagagattggttaatgctcattcc +caaacagaaaataacagggtccctatgcattagaatggaccaagcaatagtggacaaaaacatcacattgaaagcaaatt +tcagtgtgattttcaatcggcttgaagccctgatactacttagagcttttacggaagaaggagcaattgtaggcgaaatc +tcaccattaccttctcttccaggacatactgacaaggatgtcaaaaatgcaattgagatcctcatcggaggatttgaatg +gaatgataacacagttcgagtctctgaaactctacagagattcgcttggagaagcagcgatgaggatgggagatctccac +tctctacaaagtagaaacgggaaatggagagaacagttaagccagaagttcgaagaaataagatggttgattgaagaagt +acgacatagattaaaaattacggagaatagctttgagcaaataacttttatgcaagccttacaactattgcttgaagtgg +agcaagagataagaactttctcgtttcagcttatttaatga \ No newline at end of file diff --git a/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/DESCRIPTION b/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/DESCRIPTION new file mode 100644 index 00000000..0233d291 --- /dev/null +++ b/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/DESCRIPTION @@ -0,0 +1 @@ +A/Shanghai/02/2013 EPI_ISL_173625 \ No newline at end of file diff --git a/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/NOTES b/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/NOTES new file mode 100644 index 00000000..1f7b24cb --- /dev/null +++ b/static_data/flu/mut_references/H7NX/A-Shanghai-02-2013/NOTES @@ -0,0 +1,25 @@ +Two versions of this (on GISAID, NCBI Virus): + +RefSeq: + +EPI_ISL_173625 + +NC_026422 PB2 +NC_026423 PB1 +NC_026424 PA +NC_026425 HA +NC_026426 NP +NC_026427 MP +NC_026428 NS +NC_026429 NA + +EPI_ISL_141437 + +KF021594 PB2 +KF021595 PB1 +KF021596 PA +KF021597 HA +KF021598 NP +KF021599 NA +KF021600 MP +KF021601 NS \ No newline at end of file diff --git a/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/1.fa b/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/1.fa new file mode 100644 index 00000000..b9e3a71e --- /dev/null +++ b/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/1.fa @@ -0,0 +1,31 @@ +>12032|A/Hong_Kong/1073/99|EPI_ISL_140|PB2|| +gccaaaagcaggtcaattatattcaatatggaaagaataaaagaactaagaaatttgatgtcgcaatctcgcactcgcga +gatactgacaaaaaccactgtggatcatatggccataattaagaagtacacatcaggaagacaggagaagaatcccgctc +ttagaatgaaatggatgatggcgatgaaatacccgatcacagctgacaaaagaataatggagatgatccctgaaaggaat +gagcaaggccaaactctttggagcaaaacaaatgacgctggatcagacagggtaatggtatcacctctggctgtaacgtg +gtggaacagaaatggaccaacaacaagtacagtccattatccaaaggtgtataaaacctactttgaaaaggttgaaagat +taaaacacggaacctttggccctgttcatttccggaatcaagtcaaaatacgccgcagggttgacatgaaccctggccat +gcagatctcagcgctaaagaagcacaagatgtcatcatggaggtcgttttcccaaatgaagttggagccaggatattgac +atcagaatcacagctgacaataacaaaggaaaagagggaggaactcaagaattgtaatattgctcctttaatggtggcat +atatgttggaaagagaattggttcgcaagaccagattcctacccgtggctggcgggacaagcagcgtatatatagaagta +ttgcatttgactcaaggaacttgctgggagcagatgtacacaccaggaggggaggtaagaaatgatgatgttgaccaaag +tttaatcattgctgctaggaacattgtcaggagagcaacagtatcagcagacccattggcttcactcctggaaatgtgcc +atagcacacaaattggcggagtaagaatggtagacatccttaaacaaaacccaacagaagagcaagctgtagatatatgc +aaggcagcaatgggtttgaaaatcagctcatccttcagctttggagggttcactttcaaaagaacaaaggggtcttctgt +caaaagagaggaagaagtgcttacaggcaacctccaaacattgaagataaaagtacatgaaggatatgaggaattcacaa +tggttggacgaagagcaacagccattctaagaaaagcaaccagaaggatgatccaactgatagtcagcggaagggacgag +caatcaattgctgaggcaattattgtggcaatggtgttctcacaagaagattgcatggtaaaggcagtccgaggtgattt +gaatttcgtaaacagagcaaatcaacgactgaatcccatgcaccaactcctgagacactttcaaaaggatgcaaaggtgc +tgtttcaaaactggggaattgaacccatcgacaatgtcatgggtatgattggaatattgcctgacatgacccccagcacg +gaaatgtcactaagaggagtgagagttagcaaaatgggggtggatgaatattctagcactgaaagggtggtcgtgagcat +tgaccgtttcttaagggtccgagatcagcgaggaaatgtactcctatcccctgaagaagttagtgaaacacagggaatgg +aaaagttgacgataacttattcatcgtctatgatgtgggagattaacgggccagaatcagtgctagttaacacatatcaa +tggatcattaggaattgggagactgtaaagatccaatggtcccaagaacccaccatgctatacaataagatggagtttga +accatttcaatctttagtaccaaaggctgccagaagccaatatagtggatttgtgagaacgctattccagcagatgcgtg +atgttttgggaacgttcgacactgttcaaataatcaaactactaccatttgcagcagccccaccggaacagagtaggatg +caattttcttctctgactgtgaatgtgaggggatcaggaatgagaatacttgtgagaggtaactcccctgcatttaacta +caacaagacaactaagaggcttacaatacttgggaaggacgcaggtgcgcttacagaggacccagatgaaggaacagcag +gagtagagtctgcagtattgagaggatttctaatcctcggcaaagaagacaaaagatatggaccagcattaagcatcaat +gaactgagcaatcttacgaaaggggagaaagctaatgtattgatagggcaaggagacgtagtgttggtaatgaaacggaa +acgggactctagcatacttactgacagccagacagcgaccaaaagaattcggatggccatcaattagtgtcgaattgttt +aaaaacgaccttgtttctact \ No newline at end of file diff --git a/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/2.fa b/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/2.fa new file mode 100644 index 00000000..f4a3a9a5 --- /dev/null +++ b/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/2.fa @@ -0,0 +1,31 @@ +>12039|A/Hong_Kong/1073/99|EPI_ISL_140|PB1|| +gcaaaagcaggcaaaccatttgaatggatgtcaatccgactttacttttcttaaaagtgccagcgcaaaatgcaataagt +accacattcccttatactggagatcccccatatagccatggaacaggaacaggatacaccatggacacagtcaacagaac +acatcaatattcagaaaaagggaggtggacaacaaacacagagaccggagcaccccaactcaaccctattgatggaccat +tacctgaagacaatgagccgagcgggtatgcacaaacagattgtgtattggaagcaatggctttccttgaagaatcccac +ccaggactctttgaaaactcatgtcttgaaacgatggaagttgtccagcaaacgagagtggataagctgacccaaggtcg +ccagacttatgactggacattgaatagaaaccagccggctgcaactgctttggccaacaccatagaagtattcagatcga +acggtctaacagccaatgagtcaggaaggttaatagatttcctcaaggacgtaatggaatcaatggataaggaagaaatg +gaaataacaacacatttccagagaaagagaagagtgagggacaacatgaccaagaaaatggtcacacaaagaacaatagg +gaagaagaagcaaaagctgacaaaaaagagctacctaataagagcactgacactgaacacaatgacaaaagatgctgaaa +ggggaaaattgaaaagacgagcgattgcaacacccggaatgcaaatcagaggattcgtgcactttgtcgaagcactagca +aggagcatctgtgaaaaacttgagcaatctggactccccgttggagggaatgagaagaaggctaaattggcaaatgttgt +gagaaagatgatgactaactcacaagacacagagctctcctttacagttaccggagacaacaccaaatggaatgagaatc +agaatcctcgaatatttctagcaatgataacatacatcacaaggaaccaacctgaatggtttagaaatgtcttgagcatt +gcccctataatgttctcaaataaaatggcgaggttaggaaaaggatacatgttcgagagtaagagcatgaagctacggac +acaaataccagcagaaatgcttgcaaacattgacttgaaatacttcaacgaatcgacgagaaagaaaattgagaaaataa +gacctctactaatagagggcacagcctcattgagtccagggatgatgatgggcatgtttaatatgctaagtacggtctta +ggagtctcaatcttaaatcttgggcagaagaggtacaccaaaaccacatactggtgggatgggctccaatcctctgatga +tttcgctctcatagtgaatgcaccaaatcatgagggaatacaagcaggagtggatagattctataggacttgcaagctag +ttggaatcaacatgagcaaaaagaagtcttacataaatcggacaggaacatttgagttcacaagctttttctaccgctat +gggtttgtagccaacttcagcatggagctgcccagctttggagtttccggaattaatgaatcggctgacatgagcattgg +agttacagtgataaagaataatatgataaacaacgaccttggaccagcaacagcccagatggctcttcagctgttcatta +aagactacagatacacctaccgatgccacagaggtgatacacaaattcaaactagaagatcatttgaattgaagaagctg +tgggagcagacccgctcaaaggcaggactgttggtttcagatggagggccgaatttatacaacatccggaatcttcacat +tccagaagtttgcttgaagtgggagttgatggatgaagattaccagggaagactgtgtaaccctctgaacccgtttgtca +gtcataaggaagttgaatccgtcaacaatgctgtggtaatgccagcccatggtccggccaagagcatggaatatgatgcc +gttgcaactacacattcatggattcccaagagaaatcgctccattctcaacactagccaaaggggaattcttgaggatga +acaaatgtaccagaagtgctgcactctattcgagaaattcttccctagcagttcatatcggaggccagttggaatttcca +gcatgatggaggccatggtgtctagggcccgaattgatgcacggattgacttcgagtctggaaggattaagaaagaagaa +tttgctgagatcttgaagatctgttccaccattgaagagctcggacggcaagggaagtgaatttggcttgtccttcatga +aaaaatgc \ No newline at end of file diff --git a/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/3.fa b/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/3.fa new file mode 100644 index 00000000..7f9d92fe --- /dev/null +++ b/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/3.fa @@ -0,0 +1,29 @@ +>12042|A/Hong_Kong/1073/99|EPI_ISL_140|PA|| +aaagcaggtactgatccaaaatggaagactttgtgcgacagtgcttcaatccaatgattgtcgagcttgcggaaaagaca +atgaaggaatatggggaagacccgaaaattgaaacaaataagttcgctgcaatatgcacacacttagaagtctgcttcat +gtattcagacttccatttcattgacgaacgaggcgaatcaataattgtggaatctggtgatccaaatgcattgttgaagc +acaggtttgaaataattgaaggaagagaccgagcaatggcctggacagtggtgaatagcatctgcaacacaacaggagtc +gataaacccaaatttcttccggatctatacgactacaaggaaaaccgattcactgaaattggtgtgacacggagggaagt +tcacatatattacttagaaaaagctaacaagataaaatccgagaaaacacatatccacatcttttcattcactggagaag +aaatggccactaaagctgactacacccttgatgaagagagcagggcaagaataaaaaccagactattcaccataagacag +gaaatggcaagcaggggtctatgggattcctttcgtcagtccgagagaggcgaagagacaattgaagaaagatttgaaat +cacagggaccatgcgtaggcttgccgaccaaagtctcccacctaacttctccagccttgaaaactttagagcctatgtgg +atggattcaaaccgaacggctgcattgagggcaagctttctcaaatgtcgaaagaagtgaacgccagaattgagccattt +ctgaagacaacaccacgtcccctcagattgcctgatggacctccctgctcccagcggtcgaaattcttgctgatggatgc +tctgaaattaagcattgaggacccgagccatgagggggaggggataccgctatatgatgcgataaaatgcatgaaaacat +tcttcggctggagagagcccaacatcatcaagccacacgagaagggcataaatcccaattatcttctggcttggaagcag +gtgctggcagaactccaggatattgaaaatgaggataaaatcccaaaaacaaagaacatgaagaaaacaagccaattaat +gtgggcactcggggagaatatggcaccggaaaaattggactttgaggactgcaaagatattggcgatctgaaacagtatc +aaagtgatgagccagagctcagatcgatagcaagctggatccagagtgagttcaacaaggcatgtgaattgaccgattcg +agctggatagaactcgatgagataggggaagatgttgccccaattgagcacattgcaagcatgagaaggaactacttcac +agcggaagtgtctcattgcagggccactgagtacataatgaagggggtttacataaatacagctttgctcaatgcatctt +gtgcagccatggatgacttccaactgattccaatgataagcaaatgcagaacaaaagaaggaagaaggaagacaaacctg +tatgggttcattataaaaggaaggtcccatttgagaaatgatactgacgtggtgaactttgtgagtatggaattctccct +tactgacccaaggctggagccacacaaatgggaaaagtactgtgttcttgaagtaggggaaatgctcttgcggactgcaa +taggccaggtgtcaaggcccatgttcctgtatgtgagaactaacggaacctccaaaattaagatgaaatgggggatggaa +atgagacgctgccttcttcaatctcttcaacagattgagagcatgatcgaggctgagtcttctatcaaagagaaagacat +gaccaaagaattctttgaaaacagatcggagacatggccaattggagagtcacctaagggagtggaggaaggctcaatcg +ggaaggtgtgcagaaccttactagcaaaatctgtgttcaacagcctatattcatctccacaactcgaaggattttcagct +gaatcgagaaaactactactcattgttcaagcacttagggacaacctggaacctggaacctttgatcttgaagggctata +tggagcaattgaggagtgcctgattaatgatccctgggttttgcttaatgcatcttggttcaactccttcctcacacatg +cactaaaatagttgtggcaatgctactatttgctatccatactgtccaaaaaagtaccttgtttc \ No newline at end of file diff --git a/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/4.fa b/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/4.fa new file mode 100644 index 00000000..6f515652 --- /dev/null +++ b/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/4.fa @@ -0,0 +1,23 @@ +>12024|A/Hong_Kong/1073/99|EPI_ISL_140|HA|| +gcaaaagcaggggaattacttaactagcaaaatggaaacaatatcactaataactatactactagtagtaacagcaagca +atgcagataaaatctgcatcggccaccagtcaacaaactccacagaaactgtggacacgctaacagaaaccaatgttcct +gtgacacatgccaaagaattgctccacacagagcataatggaatgctgtgtgcaacaagcctgggacatcccctcattct +agacacatgcactattgaaggactagtctatggcaacccttcttgtgacctgctgttgggaggaagagaatggtcctaca +tcgtcgaaagatcatcagctgtaaatggaacgtgttaccctgggaatgtagaaaacctagaggaactcaggacacttttt +agttccgctagttcctaccaaagaatccaaatcttcccagacacaacctggaatgtgacttacactggaacaagcagagc +atgttcaggttcattctacaggagtatgagatggctgactcaaaagagcggtttttaccctgttcaagacgcccaataca +caaataacaggggaaagagcattcttttcgtgtggggcatacatcacccacccacctataccgagcaaacaaatttgtac +ataagaaacgacacaacaacaagcgtgacaacagaagatttgaataggaccttcaaaccagtgatagggccaaggcccct +tgtcaatggtctgcagggaagaattgattattattggtcggtactaaaaccaggccaaacattgcgagtacgatccaatg +ggaatctaattgctccatggtatggacacgttctttcaggagggagccatggaagaatcctgaagactgatttaaaaggt +ggtaattgtgtagtgcaatgtcagactgaaaaaggtggcttaaacagtacattgccattccacaatatcagtaaatatgc +atttggaacctgccccaaatatgtaagagttaatagtctcaaactggcagtcggtctgaggaacgtgcctgctagatcaa +gtagaggactatttggagccatagctggattcatagaaggaggttggccaggactagtcgctggctggtatggtttccag +cattcaaatgatcaaggggttggtatggctgcagatagggattcaactcaaaaggcaattgataaaataacatccaaggt +gaataatatagtcgacaagatgaacaagcaatatgaaataattgatcatgaattcagtgaggttgaaactagactcaata +tgatcaataataagattgatgaccaaatacaagacgtatgggcatataatgcagaattgctagtactacttgaaaatcaa +aaaacactcgatgagcatgatgcgaacgtgaacaatctatataacaaggtgaagagggcactgggctccaatgctatgga +agatgggaaaggctgtttcgagctataccataaatgtgatgatcagtgcatggaaacaattcggaacgggacctataata +ggagaaagtatagagaggaatcaagactagaaaggcagaaaatagagggggttaagctggaatctgagggaacttacaaa +atcctcaccatttattcgactgtcgcctcatctcttgtgcttgcaatggggtttgctgccttcctgttctgggccatgtc +caatggatcttgcagatgcaacatttgtatataa \ No newline at end of file diff --git a/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/5.fa b/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/5.fa new file mode 100644 index 00000000..788cc819 --- /dev/null +++ b/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/5.fa @@ -0,0 +1,21 @@ +>11567|A/Hong_Kong/1073/99|EPI_ISL_140|NP|| +agcagggttaataatcactcactgagtgacatcaacatcatggcgtcgcaaggcaccaaacgatcctatgaacagatgga +aactggtggagaacgccagaatgccactgagatcagggcatctgttggaagaatggttggtggaattgggaggttttacg +tacagatgtgcactgaactcaaactcagcgaccaagaaggaaggttgatccagaacagtataacaatagagagaatggtt +ctctccgcatttgatgaaaggaggaacaggtacctagaggaacatcccagtgcggggaaggacccgaagaagaccggagg +tccaatctaccgaaggagagacgggaaatgggtgagagagctgattctgtatgacaaagaggagataaggagaatttggc +gtcaagcgaacaatggagaagacgcaactgctggtctcactcatatgatgatctggcattccaacctaaatgatgccaca +taccagagaacaagagccctcgtgcggactggaatggaccccagaatgtgctctctgatgcaaggatcaaccctcccgag +gagatctggagctgctggtgcagcaataaagggagtcgggacaatggtaatggaactaattcggatgataaagcgaggca +ttaatgaccggaacttctggagaggcgataatggacgaagaacaaggattgcatatgagagaatgtgcaacatcctcaaa +gggaaatttcaaacagcagcacaaagagcaatgatggatcaggtgcgagaaagcagaaatcctgggaatgctgaaattga +agatctcatctttctggcacggtctgcactcatcctgagaggatccgtagcccataagtcctgcttgcctgcttgtgtgt +acgggctcgctgtggccagtggatatgattttgagagggaagggtactctctggttgggatagatcctttccgtctgctt +cagaacagtcaggtcttcagtcttattagaccaaatgagaatccagcacataaaagtcaattggtatggatggcatgcca +ttctgcagcatttgaggacctgagagtctcaagtttcattagaggaacaagagtgatcccaagaggacaactatccacta +gaggagttcagattgcttcaaatgagaacgtggaagcaatggattccagcactcttgaactgagaagcagatattgggct +ataaggaccaggagtggaggaaacaccaatcaacagagagcatctgcaggacaaatcagtgtacagcccactttctcagt +acagagaaatcttcccttcgaaagaccgaccattatggctgcgtttaaggggaataccgagggcagaacatctgacatga +ggactgaaatcataaggatgatggaaagtgccagaccagaagatgtgtctttccaggggcggggagtcttcgagctctcg +gacgaaaaggcaacgaacccgatcgtgccttcctttgacatgagtaatgaaggatcttatttcttcggagacaatgcaga +ggaatatgacaattgaggaaaaatacccttgtttcta \ No newline at end of file diff --git a/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/6.fa b/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/6.fa new file mode 100644 index 00000000..5ac22feb --- /dev/null +++ b/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/6.fa @@ -0,0 +1,19 @@ +>12030|A/Hong_Kong/1073/99|EPI_ISL_140|NA|| +atgaatccaaatcaaaagataatagcacttggctctgtttctataactattgcgacaatatgtttactcatgcagattgc +catcttagcaacgactatgacactacatttcaatgaatgtaccaacccatcgaacaatcaagcagtgccatgtgaaccaa +tcataatagaaaggaacataacagagatagtgcatttgaataatactaccatagagaaggaaagttgtcctaaagtagca +gaatacaagaattggtcaaaaccgcaatgtcaaattacagggttcgcccctttctccaaggacaactcaattaggctttc +tgcaggcggggatatttgggtgacaagagaaccttatgtatcgtgcggtcttggtaaatgttaccaatttgcacttgggc +agggaaccactttgaacaacaaacactcaaatggcacaatacatgataggagtccccatagaacccttttaatgaacgag +ttgggtgttccatttcatttgggaaccaaacaagtgtgcatagcatggtccagctcaagctgccatgatgggaaggcatg +gttacatgtttgtgtcactggggatgatagaaatgcgactgctagcatcatttatgatgggatgcttaccgacagtattg +gttcatggtctaagaacatcctcagaactcaggagtcagaatgcgtttgcatcaatggaacttgtacagtagtaatgact +gatggaagtgcatcaggaagggctgatactaaaatactattcattagagaagggaaaattgtccacattggtccactgtc +aggaagtgctcagcatgtggaggaatgctcctgttacccccggtatccagaagttagatgtgtttgcagagacaattgga +agggctccaatagacccgtgctatatataaatgtggcagattatagtgttgattctagttatgtgtgctcaggacttgtt +ggcgacacaccaagaaatgacgatagctccagcagcagtaactgcagggatcctaataacgagagagggggcccaggagt +gaaagggtgggcctttgacaatggaaatgatgtttggatgggacgaacaatcaagaaagattcgcgctctggttatgaga +ctttcagggtcgttggtggttggactacggctaattccaagtcacaaataaataggcaagtcatagttgacagtgataac +tggtctgggtattctggtatattctctgttgaaggaaaaacctgcatcaacaggtgtttttatgtggagttgataagagg +gagaccacaggagaccagagtatggtggacttcaaatagcatcattgtattttgtggaacttcaggtacctatggaacag +gctcatggcctgatggagcgaatatcaatttcatgtctatataagctttcgcaatttt \ No newline at end of file diff --git a/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/7.fa b/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/7.fa new file mode 100644 index 00000000..d80fc288 --- /dev/null +++ b/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/7.fa @@ -0,0 +1,14 @@ +>11556|A/Hong_Kong/1073/99|EPI_ISL_140|MP|| +ggggaattccaaaagcaggtagatattgaaagatgagtcttctaaccgaggtcgaaacgtacgttctctctatcatccca +tcaggccccctcaaagccgagatcgcgcagagacttgaggatgtttttgcagggaagaacacagatcttgaggctctcat +ggaatggctaaagacaagaccaatcctgtcacctctgactaaggggattttagggtttgtgttcacgctcaccgtgccca +gtgagcgaggactgcagcgtagacgatttgtccaaaatgccctaaatgggaatggagacccaaacaacatggacagggca +gttaaactatacaagaagctgaagagggaaatgacattccatggagcaaaggaagttgcactcagttactcaactggtgc +gcttgccagttgcatgggtctcatatacaaccggatgggaacagtgaccacagaagtggctcttggcctagtatgtgcca +cttgtgaacagattgctgatgcccaacatcggtcccacaggcagatggcgactaccaccaacccactaatcaggcatgag +aacagaatggtactagccagcactacggctaaggccatggagcagatggctggatcaagtgagcaggcagcagaagccat +ggaagtcgcaagtcaggctaggcaaatggtgcaggctatgaggacaattgggactcaccctagttccagtgcaggtctaa +aagatgatcttattgaaaatttgcaggcttaccagaaacggatgggagtgcaaatgcagagattcaagtgatcctctcgt +tgttgcagcaagtatcattgggatattgcacttgatattgtggattcttgatcgtcttttcttcaaatgcatttatcgtc +gctttaaatacggtttgaaaagagggccttctacggaaggagtgcctgagtctatgagggaagagtatcggcaggaacag +cagaatgctgtggatgttgacgatggtcattttgtcaacatagagctggagtaaaagatcttcct \ No newline at end of file diff --git a/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/8.fa b/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/8.fa new file mode 100644 index 00000000..ff286cf6 --- /dev/null +++ b/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/8.fa @@ -0,0 +1,13 @@ +>11562|A/Hong_Kong/1073/99|EPI_ISL_140|NS|| +agcaaaagcagggtgacaaagacataatggattccaacactgtgtcaagctttcaggtagactgctttctttggcatgtc +cgcaaacgatttgcagaccaagaactgggtgatgccccattccttgaccggcttcgccgagatcagaagtccctaagagg +aagaggcagcactcttggtctggacatcagaactgccactcgtgaaggaaagcatatagtggagcggattctggaggaag +aatctgacgaggcacttaaaatgactatcgcttcagtgcctgcttcacgctacctaactgaaatgactcttgaggaaatg +tcaagggattggttaatgctcattcccaagcagaaagtgacagggcccctttgcattagaatggaccaggcagtaatggg +taaaaccatcatattgaaagcaaactttagtgtgatttttaatcgacttgaagctctgatactacttagagcgtttacag +atgaaggagcaatagtgggcgaaatctcaccattaccttcccttccaggacatactgacgaggatgtcaaaaatgcaatt +ggggtcctcatcggaggacttgaatggaatgataacacagttcgagtctctgaaactctacagagattcacttggagaag +cagtgatgagaatgggagatctccactccctccaaaacagaaacggaaagtggagagaacaattgagccagaagtttgaa +gagataagatggttaattgaagaaatgcgacataggttaagaattacagagaatagctttgagcaaataacctttatgca +agccttacaactattgcttgaagtggagcaagagataagaactttctcgtttcagcttatttaatgataaaaaacaccct +tgtttctact \ No newline at end of file diff --git a/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/NOTES b/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/NOTES new file mode 100644 index 00000000..371dbd5a --- /dev/null +++ b/static_data/flu/mut_references/H9NX/A-Hong-Kong-1073-99/NOTES @@ -0,0 +1,30 @@ +RefSeq: + +NC_004907 MP Derived from AJ278646 EPI11556 +NC_004905 NP Derived from AJ289871 EPI11567 +NC_004906 NS Derived from AJ278649 EPI11562 +NC_004908 HA Identical to AJ404626 EPI12024 +NC_004909 NA Identical to AJ404629 EPI12030 +NC_004910 PB2 Identical to AJ404630 EPI12032 +NC_004911 PB1 Identical to AJ404634 EPI12039 +NC_004912 PA Identical to AJ404637 EPI12042 + +GISAID: + +segment identifier length accession # INSDC +PB2 A/Hong_Kong/1073/99 2341 EPI7911 AF258835 +PB2 A/Hong_Kong/1073/99 2341 EPI12032 AJ404630 +PB1 A/Hong_Kong/1073/99 2341 EPI7873 AF258816 +PB1 A/Hong_Kong/1073/99 2328 EPI12039 AJ404634 +PA A/Hong_Kong/1073/99 2233 EPI7811 AF257191 +PA A/Hong_Kong/1073/99 2225 EPI12042 AJ404637 +HA A/Hong_Kong/1073/99 960 EPI451 AB080226 +HA A/Hong_Kong/1073/99 1714 EPI12024 AJ404626 +NP A/Hong_Kong/1073/99 1565 EPI7702 AF255742 +NP A/Hong_Kong/1073/99 1557 EPI11567 AJ289871 +NA A/Hong_Kong/1073/99 1418 EPI12030 AJ404629 +MP A/Hong_Kong/1073/99 1027 EPI7640 AF255363 +MP A/Hong_Kong/1073/99 1025 EPI11556 AJ278646 +MP A/Hong_Kong/1073/99 1026 EPI11557 AJ278647 +NS A/Hong_Kong/1073/99 890 EPI7754 AF256176 +NS A/Hong_Kong/1073/99 890 EPI11562 AJ278649 diff --git a/static_data/flu/proteins.csv b/static_data/flu/proteins.csv index c16d9564..81f7e880 100644 --- a/static_data/flu/proteins.csv +++ b/static_data/flu/proteins.csv @@ -152,7 +152,7 @@ H7NX,A-Shanghai-02-2013,PB1,2,1..2274,1,0,[], H7NX,A-Shanghai-02-2013,PB1-F2,2,95..367,1,0,[], H7NX,A-Shanghai-02-2013,PA,3,1..2151,1,0,[], H7NX,A-Shanghai-02-2013,PA-X,3,1..570;572..760,1,0,[], -H7NX,A-Shanghai-02-2013,HA,4,1..1683,1,16,"[{""name"": ""signal peptide"", ""ranges"": [[1, 18]]}, {""name"": ""HA1"", ""ranges"": [[19, 339]]}, {""name"": ""HA2"", ""ranges"": [[340, 560]]}]", +H7NX,A-Shanghai-02-2013,HA,4,1..1683,1,18,"[{""name"": ""signal peptide"", ""ranges"": [[1, 18]]}, {""name"": ""HA1"", ""ranges"": [[19, 339]]}, {""name"": ""HA2"", ""ranges"": [[340, 560]]}]", H7NX,A-Shanghai-02-2013,NP,5,1..1497,1,0,[], H7NX,A-Shanghai-02-2013,NA,6,1..1398,1,0,[], H7NX,A-Shanghai-02-2013,M1,7,1..759,1,0,[], @@ -163,14 +163,14 @@ H9NX,A-Hong-Kong-1073-99,PB2,1,28..2307,1,0,[], H9NX,A-Hong-Kong-1073-99,PB1,2,24..2300,1,0,[], H9NX,A-Hong-Kong-1073-99,PB1-F2,2,118..390,1,0,[], H9NX,A-Hong-Kong-1073-99,PA,3,21..2171,1,0,[], -H9NX,A-Hong-Kong-1073-99,HA,4,1..1714,1,16,"[{""name"": ""signal peptide"", ""ranges"": [[1, 18]]}, {""name"": ""HA1"", ""ranges"": [[19, 338]]}, {""name"": ""HA2"", ""ranges"": [[339, 560]]}]", +H9NX,A-Hong-Kong-1073-99,HA,4,1..1714,1,18,"[{""name"": ""signal peptide"", ""ranges"": [[1, 18]]}, {""name"": ""HA1"", ""ranges"": [[19, 338]]}, {""name"": ""HA2"", ""ranges"": [[339, 560]]}]", H9NX,A-Hong-Kong-1073-99,NP,5,40..1536,1,0,[], H9NX,A-Hong-Kong-1073-99,NA,6,1..1404,1,0,[], H9NX,A-Hong-Kong-1073-99,M1,7,33..791,1,0,[], H9NX,A-Hong-Kong-1073-99,M2,7,33..59;748..1014,1,0,[], H9NX,A-Hong-Kong-1073-99,NEP,8,27..56;529..864,1,0,[], H9NX,A-Hong-Kong-1073-99,NS1,8,27..719,1,0,[], -B-yam,B-Massachusetts-02-2012,HA,4,1..1755,1,0,[], +B-yam,B-Massachusetts-02-2012,HA,4,1..1755,1,15,"[{""name"": ""signal peptide"", ""ranges"": [[1, 15]]}, {""name"": ""HA1"", ""ranges"": [[16, 361]]}, {""name"": ""HA2"", ""ranges"": [[362, 584]]}]", B-yam,B-Massachusetts-02-2012,NA,6,1..1401,1,0,[], B-yam,B-Massachusetts-02-2012,NB,6,3..296,1,0,[], B-yam,B-Massachusetts-02-2012,NEP,8,1..33;689..1024,1,0,[], @@ -178,7 +178,7 @@ B-yam,B-Massachusetts-02-2012,NS1,8,1..846,1,0,[], B-yam,B-Phuket-3073-2013,PB2,1,1..2313,1,0,[], B-yam,B-Phuket-3073-2013,PB1,2,1..2259,1,0,[], B-yam,B-Phuket-3073-2013,PA,3,1..2181,1,0,[], -B-yam,B-Phuket-3073-2013,HA,4,1..1755,1,0,[], +B-yam,B-Phuket-3073-2013,HA,4,1..1755,1,15,"[{""name"": ""signal peptide"", ""ranges"": [[1, 15]]}, {""name"": ""HA1"", ""ranges"": [[16, 361]]}, {""name"": ""HA2"", ""ranges"": [[362, 584]]}]", B-yam,B-Phuket-3073-2013,NP,5,1..1683,1,0,[], B-yam,B-Phuket-3073-2013,NA,6,34..1434,1,0,[], B-yam,B-Phuket-3073-2013,NB,6,27..329,1,0,[], @@ -186,7 +186,7 @@ B-yam,B-Phuket-3073-2013,M,7,1..747,1,0,[], B-yam,B-Phuket-3073-2013,BM2,7,747..1076,1,0,[], B-yam,B-Phuket-3073-2013,NEP,8,1..33;689..1024,1,0,[], B-yam,B-Phuket-3073-2013,NS1,8,1..846,1,0,[], -B-yam,B-Wisconsin-01-2010,HA,4,1..1755,1,0,[], +B-yam,B-Wisconsin-01-2010,HA,4,1..1755,1,15,"[{""name"": ""signal peptide"", ""ranges"": [[1, 15]]}, {""name"": ""HA1"", ""ranges"": [[16, 361]]}, {""name"": ""HA2"", ""ranges"": [[362, 584]]}]", B-yam,B-Wisconsin-01-2010,NA,6,1..1401,1,0,[], B-yam,B-Wisconsin-01-2010,NB,6,3..296,1,0,[], B-yam,B-Wisconsin-01-2010,NEP,8,1..33;689..1024,1,0,[], @@ -194,7 +194,7 @@ B-yam,B-Wisconsin-01-2010,NS1,8,1..846,1,0,[], B-vic,B-Austria-1359417-2021,PB2,1,1..2313,1,0,[], B-vic,B-Austria-1359417-2021,PB1,2,1..2259,1,0,[], B-vic,B-Austria-1359417-2021,PA,3,1..2181,1,0,[], -B-vic,B-Austria-1359417-2021,HA,4,1..1749,1,0,[], +B-vic,B-Austria-1359417-2021,HA,4,1..1749,1,15,"[{""name"": ""signal peptide"", ""ranges"": [[1, 15]]}, {""name"": ""HA1"", ""ranges"": [[16, 359]]}, {""name"": ""HA2"", ""ranges"": [[360, 582]]}]", B-vic,B-Austria-1359417-2021,NP,5,1..1683,1,0,[], B-vic,B-Austria-1359417-2021,NA,6,8..1408,1,0,[], B-vic,B-Austria-1359417-2021,NB,6,1..303,1,0,[], @@ -202,8 +202,8 @@ B-vic,B-Austria-1359417-2021,M,7,1..747,1,0,[], B-vic,B-Austria-1359417-2021,BM2,7,747..1076,1,0,[], B-vic,B-Austria-1359417-2021,NEP,8,1..36;692..1027,1,0,[], B-vic,B-Austria-1359417-2021,NS1,8,1..849,1,0,[], -B-vic,B-Brisbane-60-2008,HA,4,34..1791,1,0,[], -B-vic,B-Colorado-06-2017,HA,4,34..1785,1,0,[], +B-vic,B-Brisbane-60-2008,HA,4,34..1791,1,15,"[{""name"": ""signal peptide"", ""ranges"": [[1, 15]]}, {""name"": ""HA1"", ""ranges"": [[16, 362]]}, {""name"": ""HA2"", ""ranges"": [[363, 585]]}]", +B-vic,B-Colorado-06-2017,HA,4,34..1785,1,15,"[{""name"": ""signal peptide"", ""ranges"": [[1, 15]]}, {""name"": ""HA1"", ""ranges"": [[16, 360]]}, {""name"": ""HA2"", ""ranges"": [[361, 583]]}]", B-vic,B-Colorado-06-2017,NA,6,54..1454,1,0,[], B-vic,B-Colorado-06-2017,NB,6,47..349,1,0,[], B-vic,B-Colorado-06-2017,M,7,25..771,1,0,[], @@ -211,7 +211,7 @@ B-vic,B-Colorado-06-2017,BM2,7,771..1100,1,0,[], B-vic,B-Washington-02-2019,PB2,1,10..2322,1,0,[], B-vic,B-Washington-02-2019,PB1,2,8..2266,1,0,[], B-vic,B-Washington-02-2019,PA,3,16..2196,1,0,[], -B-vic,B-Washington-02-2019,HA,4,20..1768,1,0,[], +B-vic,B-Washington-02-2019,HA,4,20..1768,1,15,"[{""name"": ""signal peptide"", ""ranges"": [[1, 15]]}, {""name"": ""HA1"", ""ranges"": [[16, 359]]}, {""name"": ""HA2"", ""ranges"": [[360, 582]]}]", B-vic,B-Washington-02-2019,NP,5,47..1729,1,0,[], B-vic,B-Washington-02-2019,NA,6,40..1440,1,0,[], B-vic,B-Washington-02-2019,NB,6,33..335,1,0,[], diff --git a/static_data/flu/proteins_processed.json b/static_data/flu/proteins_processed.json index a719131a..f7ceef12 100644 --- a/static_data/flu/proteins_processed.json +++ b/static_data/flu/proteins_processed.json @@ -6970,14 +6970,14 @@ ] ], "protein_coding": true, - "residue_offset": 16, + "residue_offset": 18, "domains": [ { "name": "signal peptide", "ranges": [ [ - -15, - 2 + -17, + 0 ] ], "row": 0, @@ -6992,8 +6992,8 @@ "name": "HA1", "ranges": [ [ - 3, - 323 + 1, + 321 ] ], "row": 1, @@ -7008,8 +7008,8 @@ "name": "HA2", "ranges": [ [ - 324, - 544 + 322, + 542 ] ], "row": 0, @@ -7025,8 +7025,8 @@ "len_nt": 1683, "len_aa": 561, "residue_offset_range": [ - -15, - 545 + -17, + 543 ], "nt_range": [ 1, @@ -7452,14 +7452,14 @@ ] ], "protein_coding": true, - "residue_offset": 16, + "residue_offset": 18, "domains": [ { "name": "signal peptide", "ranges": [ [ - -15, - 2 + -17, + 0 ] ], "row": 0, @@ -7474,8 +7474,8 @@ "name": "HA1", "ranges": [ [ - 3, - 322 + 1, + 320 ] ], "row": 1, @@ -7490,8 +7490,8 @@ "name": "HA2", "ranges": [ [ - 323, - 544 + 321, + 542 ] ], "row": 0, @@ -7507,8 +7507,8 @@ "len_nt": 1714, "len_aa": 571, "residue_offset_range": [ - -15, - 555 + -17, + 553 ], "nt_range": [ 1, @@ -7786,14 +7786,63 @@ ] ], "protein_coding": true, - "residue_offset": 0, - "domains": [], + "residue_offset": 15, + "domains": [ + { + "name": "signal peptide", + "ranges": [ + [ + -14, + 0 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1, + 45 + ] + ] + }, + { + "name": "HA1", + "ranges": [ + [ + 1, + 346 + ] + ], + "row": 1, + "nt_ranges": [ + [ + 46, + 1083 + ] + ] + }, + { + "name": "HA2", + "ranges": [ + [ + 347, + 569 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1084, + 1752 + ] + ] + } + ], "notes": "", "len_nt": 1755, "len_aa": 585, "residue_offset_range": [ - 1, - 585 + -14, + 570 ], "nt_range": [ 1, @@ -8096,14 +8145,63 @@ ] ], "protein_coding": true, - "residue_offset": 0, - "domains": [], + "residue_offset": 15, + "domains": [ + { + "name": "signal peptide", + "ranges": [ + [ + -14, + 0 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1, + 45 + ] + ] + }, + { + "name": "HA1", + "ranges": [ + [ + 1, + 346 + ] + ], + "row": 1, + "nt_ranges": [ + [ + 46, + 1083 + ] + ] + }, + { + "name": "HA2", + "ranges": [ + [ + 347, + 569 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1084, + 1752 + ] + ] + } + ], "notes": "", "len_nt": 1755, "len_aa": 585, "residue_offset_range": [ - 1, - 585 + -14, + 570 ], "nt_range": [ 1, @@ -8406,14 +8504,63 @@ ] ], "protein_coding": true, - "residue_offset": 0, - "domains": [], + "residue_offset": 15, + "domains": [ + { + "name": "signal peptide", + "ranges": [ + [ + -14, + 0 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1, + 45 + ] + ] + }, + { + "name": "HA1", + "ranges": [ + [ + 1, + 346 + ] + ], + "row": 1, + "nt_ranges": [ + [ + 46, + 1083 + ] + ] + }, + { + "name": "HA2", + "ranges": [ + [ + 347, + 569 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1084, + 1752 + ] + ] + } + ], "notes": "", "len_nt": 1755, "len_aa": 585, "residue_offset_range": [ - 1, - 585 + -14, + 570 ], "nt_range": [ 1, @@ -8716,14 +8863,63 @@ ] ], "protein_coding": true, - "residue_offset": 0, - "domains": [], + "residue_offset": 15, + "domains": [ + { + "name": "signal peptide", + "ranges": [ + [ + -14, + 0 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1, + 45 + ] + ] + }, + { + "name": "HA1", + "ranges": [ + [ + 1, + 344 + ] + ], + "row": 1, + "nt_ranges": [ + [ + 46, + 1077 + ] + ] + }, + { + "name": "HA2", + "ranges": [ + [ + 345, + 567 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1078, + 1746 + ] + ] + } + ], "notes": "", "len_nt": 1749, "len_aa": 583, "residue_offset_range": [ - 1, - 583 + -14, + 568 ], "nt_range": [ 1, @@ -9026,14 +9222,63 @@ ] ], "protein_coding": true, - "residue_offset": 0, - "domains": [], + "residue_offset": 15, + "domains": [ + { + "name": "signal peptide", + "ranges": [ + [ + -14, + 0 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 34, + 78 + ] + ] + }, + { + "name": "HA1", + "ranges": [ + [ + 1, + 347 + ] + ], + "row": 1, + "nt_ranges": [ + [ + 79, + 1119 + ] + ] + }, + { + "name": "HA2", + "ranges": [ + [ + 348, + 570 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1120, + 1788 + ] + ] + } + ], "notes": "", "len_nt": 1758, "len_aa": 586, "residue_offset_range": [ - 1, - 586 + -14, + 571 ], "nt_range": [ 34, @@ -9065,14 +9310,63 @@ ] ], "protein_coding": true, - "residue_offset": 0, - "domains": [], + "residue_offset": 15, + "domains": [ + { + "name": "signal peptide", + "ranges": [ + [ + -14, + 0 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 34, + 78 + ] + ] + }, + { + "name": "HA1", + "ranges": [ + [ + 1, + 345 + ] + ], + "row": 1, + "nt_ranges": [ + [ + 79, + 1113 + ] + ] + }, + { + "name": "HA2", + "ranges": [ + [ + 346, + 568 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1114, + 1782 + ] + ] + } + ], "notes": "", "len_nt": 1752, "len_aa": 584, "residue_offset_range": [ - 1, - 584 + -14, + 569 ], "nt_range": [ 34, @@ -9363,14 +9657,63 @@ ] ], "protein_coding": true, - "residue_offset": 0, - "domains": [], + "residue_offset": 15, + "domains": [ + { + "name": "signal peptide", + "ranges": [ + [ + -14, + 0 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 20, + 64 + ] + ] + }, + { + "name": "HA1", + "ranges": [ + [ + 1, + 344 + ] + ], + "row": 1, + "nt_ranges": [ + [ + 65, + 1096 + ] + ] + }, + { + "name": "HA2", + "ranges": [ + [ + 345, + 567 + ] + ], + "row": 0, + "nt_ranges": [ + [ + 1097, + 1765 + ] + ] + } + ], "notes": "", "len_nt": 1749, "len_aa": 583, "residue_offset_range": [ - 1, - 583 + -14, + 568 ], "nt_range": [ 20, diff --git a/static_data/flu/reference.json b/static_data/flu/reference.json index 82eb8eae..898f6bb9 100644 --- a/static_data/flu/reference.json +++ b/static_data/flu/reference.json @@ -799,5 +799,146 @@ } }, "description": "A/Victoria/361/2011 EPI2120562 (2012-2013)" + }, + "A-Goose-Guangdong-1-96": { + "name": "A-Goose-Guangdong-1-96", + "subtype": "H5NX", + "segments": { + "1": { + "name": "5779|A/Goose/Guangdong/1/96|EPI_ISL_1254|PB2||", + "sequence": "AGCAAAAGCAGGTCAATTATATTCAATATGGAAAGAATAAAAGAACTAAGAGATCTAATGTCGCAGTCCCGCACTCGCGAGATACTAACAAAAACCACTGTGGATCATATGGCCATAATCAAGAAATACACATCAGGAAGACAAGAGAAGAACCCTGCTCTCAGAATGAAATGGATGATGGCAATGAAATATCCAATCACAGCAGACAAGAGAATAATGGAGATGATTCCTGAAAGGAATGAGCAAGGACAAACGCTTTGGAGCAAGACAAATGATGCTGGGTCGGACAGAGTGATGGTGTCTCCCCTAGCTGTAACTTGGTGGAACAGGAATGGGCCGACAACAAGTACAGTCCATTATCCAAAGGTTTACAAAACATACTTTGAGAAGGTTGAAAGGTTAAAACATGGAACCTTCGGTCCCGTTCATTTCCGAAACCAAGTTAAAATACGTCGCCGGGTGGATATAAACCCGGGCCATGCAGATCTCAGTGCTAAAGAAGCACAAGATGTTATCATGGAGGTCGTTTTCCCAAATGAAGTGGGAGCTAGAATATTGACATCAGAGTCGCAATTGACAATAACAAAAGAGAAGAAAGAAGAGCTCCAGGATTGTAAAATTGCTCCTTTAATGGTGGCATACATGTTGGAAAGAGAACTGGTCCGCAAAACCAGATTTCTACCGGTAGCAGGCGGAACAAGCAGTGTGTACATTGAGGTATTGCATTTGACTCAAGGGACCTGTTGGGAACAGATGTACACTCCCGGCGGAGAAGTAAGAAATGATGATGTTGACCAGAGTTTGATCATCGCTGCCAGAAACATTGTTAGGAGAGCAACAGTATCAGCGGACCCACTGGCATCACTCTTGGAGATGTGTCACAGCACACAAATTGGGGGAATAAGGATGGTGGACATCCTTAGGCAAAACCCAACTGAGGAGCAAGCTGTGGATATATGCAAAGCAGCAATGGGTTTGAGGATCAGTTCATCCTTTAGCTTTGGAGGCTTCACTTTCAAAAGAACAAATGGATCATCCGTCAAGAAGGAAGAGGAAGTGCTTACAGGCAACCTCCAAACATTGAAAATAAAAGTACATGAGGGGTATGAAGAATTCACAATGGTTGGGCGGAGAGCAACAGCTATCCTGAGGAAAGCAACTAGAAGGCTGATTCAGTTGATAGTAAGTGGAAGAGATGAACAATCAATCGCTGAAGCGATCATTGTAGCAATGGTGTTCTCACAGGAGGATTGCATGATAAAGGCAGTCCGAGGCGATCTGAATTTCGTGAACAGAGCAAACCAAAGATTGAACCCCATGCATCAACTCCTGAGGCACTTCCAAAAAGATGCAAAAGTGCTGTTTCAGAACTGGGGAATTGAACCTATTGACAATGTCATGGGGATGATCGGAATATTACCTGACATGACTCCAAGCGCAGAGATGTCACTGAGAGGAGTGAGAGTTAGTAAGATGGGAGTAGATGAATATTCCAGCACGGAGAGAGTGGTGGTGAGTATTGACCGTTTCTTGAGGGTCCGAGATCAGCAGGGGAACGTACTCTTATCTCCTGAAGAGGTTAGTGAAACACAGGGAACAGAGAAGTTGACAATAACATATTCATCCTCAATGATGTGGGAAATCAACGGTCCTGAGTCAGTGCTTGTTAACACTTATCAATGGATCATCAGGAATTGGGAGACTGTAAAGATTCAATGGTCTCAAGATCCCACAATGCTGTACAATAAGATGGAGTTTGAATCGTTCCAATCCTTGGTGCCAAAGGCTGCCAGAAGCCAATATAGTGGATTTGTGAGAACACTATTCCAACAGATGCGTGATGTTTTGGGGACATTTGATACTGTCCAAATAATCAAGCTGCTACCATTTGCAGCAGCCCCACCGGAGCCGAGCAGAATGCAGTTTTCTTCTCTAACTGTGAATGTGAGAGGCTCAGGAATGAGAATACTCGTGAGGGGTAACTCCCCCGTGTTCAACTACAACAAGGCAACCAAAAGGCTTACAGTCCTCGGAAAGGACGCAGGTGCATTAACAGAAGATCCAGACGAGGGAACAGCCGGGGTGGAATCTGCAGTATTGAGGGGATTCCTAATTCTAGGCAGAGAGGACAAAAGATATGGACCCGCATTGAGCATCAATGAACTGAGCAATCTTGCAAAAGGGGAGAAGGCTAATGTATTGATAATGCAAGGAGACGTGGTGTTGGTAATGAAACGGAAACGGGACTTTAGCATACTTACTGACAGCCAGACAGCGACCAAAAGAATTCGGATGGCCATCAATTAGTGTTGAATAGTTTAAAAACGACCTTGTTTCTACT", + "description": "" + }, + "2": { + "name": "5781|A/Goose/Guangdong/1/96|EPI_ISL_1254|PB1||", + "sequence": "AGCAAAAGCAGGCAAACCATTTGAATGGATGTCAATCCGACTTTACTTTTCTTAAAAGTGCCAGCGCAAAATGCTATAAGTACCACATTCCCTTATACTGGAGATCCTCCATACAGCCATGGAACAGGAACAGGATACACCATGGACACAGTCAACAGAACACATCAATATTCAGAAAAGGGGAAATGGACAACGAACACAGAGACTGGAGCACCCCAACTCAATCCGATTGATGGACCACTACCTGAGGATAATGAGCCGAGTGGGTATGCACAAACAGATTGTGTATTGGAAGCAATGGCTTTCCTTGAAGAATCCCACCCAGGGATCTTTGAAAACTCGTGTCTTGAAACGATGGAAGTTGTTCAGCAAACAAGAGTGGATAAGCTGACCCAAGGTCGCCAAACCTATGACTGGACATTGAAAAGAAACCAGCCGGCTGCAACCGCTTTGGCCAACACTATAGAGGTCTTCAGATCGAATGGTCTAACAGCCAATGAATCGGGAAGGCTAATAGATTTCCTCAAAGACGTGATGGAATCAATGGATAAGGGAGAAATGGAAATAATAACACATTTCCAGAGAAAGAGAAGAGTGAGGGACAACATGACCAAGAAAATGGTCACACAAAGAACAATAGGGAAGAAAAAACAAAGGCTGAACAAAAGGAGCTACCTAATAAGAGCACTGACACTGAACACAATGACAAAAGACGCAGAAAGAGGCAAATTGAAGAGGCGGGCAATTGCAACACCCGGGATGCAAATCAGAGGATTCGTGTACTTTGTCGAAACACTAGCGAGGAGTATCTGTGAGAAACTTGAGCAATCTGGACTCCCCGTCGGAGGGAATGAAAAGAAGGCTAAATTGGCAAATGTCGTGAGGAAGATGATGACTAACTCACAAGATACAGAGCTCTCTTTTACAATTACTGGAGACAACACCAAATGGAATGAGAATCAGAACCCTCGGATGTTTCTAGCAATGATAACATACATCACAAGGAACCAACCTGAATGGTTTAGAAATGTCTTAAGCATTGCTCCTATAATGTTCTCAAACAAGATGGCAAGATTAGGGAAAGGATACATGTTCGAAAGTAAGAGCATGAAGCTACGGACACAAATACCAGCAGAAATGCTTGCAAGCATTGACTTGAAATACTTCAACGAATCAACGAGAAAGAAAATCGAGAAAATAAGACCTCTACTAATAGATGGCACAGCCTCATTGAGTCCTGGAATGATGATGGGCATGTTCAATATGCTGAGTACAGTCTTAGGAGTTTCAATCCTGAATCTTGGGCAGAAGAGGTACACCAAAACCACATACTGGTGGGACGGACTCCAATCCTCTGATGATTTCGCTCTCATAGTGAATGCACCAAATCATGAGGGAATAGAAGCAGGGGTGGATAGGTTCTATAGGACTTGCAAACTAGTTGGAATCAATATGACCAAGAAGAAGTCTTACATAAATCGGACAGGAACATGTGAATTCACAAGCTTCTTCTACCGCTATGGGTTCGTAGCCAACTTCAGTATGGAGCTGCCCAGCTTTGGAGTGTCTGGGATTAATGAATCGGCTGACATGAGCATTGGTGTTACAGTGATAAAGAACAATATGATGGACAACGACCTTGGACCAGCAACAGCTCAGATGGCTCTTCAGCTATTCATTAAGGACTACAGATACCCATACCGATGCCACAGGGGGGATACACAAATCCAAACGAGGAGATCATTCGAGCTGAAGAAGCTGTGGGAGCAGACCCGCTCAAAGGCAGGACTGTTGGTTTCAGATGGAGGACCAAACCCATACAATATCCGGAATCTCCACATTCCGGAGGCTGGCTTGAAGTGGGAATTGATGGATGAAGACTACCAGGGCAGACTGTGTAATCCTCTGAACCCGTTTGTTAGTCATAAGGAAATTGAGTCTGTCAACAATGCTGTGGTAATGCCAGCTCATGGCCCAGCCAAGAGCATGGAATATGATGCAGTTGCGACTACACATTCATGGATTCCCAAGAGGAATCGTTCCATTCTCAACACCAGCCAAAGGGGGATTCTTGAGGATGAACAGATGTATCAGAAGTGCTGCAATCTATTCGAGAAATTCTTCCCTAGCAGTTCATATCGGAGGCCAGTTGGAATTTCCAGCATGGTGGAGGCCATGGTGTCTAGGGCCCGAATTGATGCACGAATTGACTTCGAGTCTGGAAGGATTAAGAAAGAAGAGTTTGCTGAGATCATGAAGATCTGTTCCACCATTGAAGAGCTCGGACGGCAAAAATAGTGAATTTAGCTTGTCCTTCATGAAAAAATGCCTTGTTTCTACT", + "description": "" + }, + "3": { + "name": "5783|A/Goose/Guangdong/1/96|EPI_ISL_1254|PA||", + "sequence": "AGCAAAAGCAGGTACTGATCCAAAATGGAAGACTTTGTGCGACAATGCTTCAATCCAATGATTGTCGAGCTTGCGGAAAAGGCAATGAAAGAATATGGGGAAGATCCGAAAATCGAAACGAACAAATTTGCCGCAATATGCACGCACTTAGAAGTCTGTTTCATGTATTCAGATTTCCACTTTATTGATGAACGGGGCGAATCAACAATTATAGAATCTGGCGATCCCAATGCATTATTGAAACACCGGTTTGAAATAATCGAAGGGAGGGACCGAACAATGGCCTGGACAGTGGTGAATAGTATCTGCAACACCACAGGAGTTGAGAAGCCTAAATTTCTCCCAGATTTGTATGACTACAAGGAGAACCGATTTATTGAAATTGGAGTGACACGGAGGGAAGTTCACACATACTATCTAGAAAAAGCCAACAAGATAAAATCTGAGAAGACACACATTCACATATTCTCATTCACTGGAGAGGAAATGGCCACCAAAGCGGACTACACCCTTGATGAAGAAAGCAGGGCCCGAATCAAAACCAGGCTGTTCACTATAAGGCAGGAAATGGCCAGTAGGGGTTTATGGGATTCCTTTCGTCAGTCCGAGAGAGGCGAAGAGACAGTTGAAGAAAGATTTGAAATCACAGGGACTATGTGCAGGCTTGCCGACCAAAGTCTCCCACCTAATTTCTCCAGCCTTGAAAAATTTAGAGCCTATGTGGATGGATTCGAACCGAACGGCTGCATTGAGGGCAAGCTTTCTCAAATGTCGAAAGAAGTAAACGCCAGAATTGAGCCATTTCTGAAGACAACACCACGCCCTCTTAGATTACCTGATGGGCCTCCCTGCTCTCAGCGGTCGAAGTTTTTGCTGATGGATGCCCTTAAATTAAGCATCGAAGACCCGAGTCATGAGGGGGAGGGGATACCGCTATATGATGCAATCAAATGCATGAAAACATTTTTCGGCTGGAAAGAGCCCAACATTGTAAAACCACATGAAAAAGGCATAAACCCCAATTACCTCCTGGCTTGGAAGCAGGTGCTGGCAGAGCTCCAAGATATTGAAAACGAGGAGAAAATTCCAAAGACAAAGAACATGAGGAAAACAAGCCAATTGAAGTGGGCACTTGGTGAGAATATGGCACCAGAGAAAGTAGACTTTGAGGATTGCAAAGATGTTAGCGATCTAAGGCAGTATGACAGTGATGAACCAAAGCCTAGATCACTAGCAAGCTGGATCCAGAGTGAATTCAACAAGGCATGCGAATTGACAGATTCAAGTTGGATTGAACTTGATGAAATAGGGGAAGACGTTGCTCCAATTGAGCACATTGCAAGTATGAGAAGGAACTATTTCACAGCGGAAGTATCCCATTGCAGGGCTACTGAATACATAATGAAGGGAGTGTACATAAACACAGCTTTGTTGAATGCATCCTGTGCAGCCATGGATGACTTCCAACTGATCCCAATGATAAGCAAATGCAGAACCAAAGAAGGAAGACGGAAAACTAACCTGTATGGATTCCTTATAAAAGGAAGATCCCATTTGAGAAATGACACCGATGTGGTAAACTTTGTGAGTATGGAATTCTCTCTTACTGATCCGAGGCTGGAGCCACACAGATGGGAAAAGTACTGCGTTCTTCGGATAGGAGACATGCTCTTACGGACTGAAATAGGCCAAGTGTCAAGGCCCATGTTTCTTTATGTGAGAACCAATGGAACCTCCAAGATCAAGATGAAATGGGGCATGGAAATGAGGCGATGCCCTTTTCAATCCCTTCAACAGATTGAGAGCATGATTGAGGCCGAGTCTTCTGTCAAAGAAAAAGACATGACTAAAGAATTCTTTGAAAACAAATCAGAAACATGGCCAATTGGAGAATCACCCAAGGGAGTGGAGGAAGGCTCCATCGGGAAGGTGTGCAGAACCTTACTGGCTAAATCTGTTTTCAACAGTCTATATGCATCTCCACAACTCGAGGGGTTTTCAGCTGAATCAAGAAAATTGCTTCTCATTGTTCAGGCACTTAGGGACAACCTGGAACCTGGAACCTTCGATCTTGGGGGGCTATATGAAGCAATTGAGGAGTGCCTGATTAATGATCCCTGGGTTTTGCTTAATGCATCTTGGTTCAACTCCTTCCTCACACATGCACTAAGATAGTTGTGGCAATGCTACTATTTGCTATCCATACTGTCCAAAAAAGTACCTTGTTTCTACT", + "description": "" + }, + "4": { + "name": "5789|A/Goose/Guangdong/1/96|EPI_ISL_1254|HA||", + "sequence": "GCAGGGGTATAATCTGTCAAAATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTCAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAATGGGAAGCTCTGCGATCTAAATGGAGTGAAGCCTCTCATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCTATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAACAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCATGGGAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTAGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACTTACATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATACCCCTCAGAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTGGAAAGGAGGATAGAGAATTTAAACAAGCAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTATGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAATGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATTTGCATTTAAATTTGTGAGTTCAGATTGTAGTTAAAAACACC", + "description": "" + }, + "5": { + "name": "5785|A/Goose/Guangdong/1/96|EPI_ISL_1254|NP||", + "sequence": "AGCAAAAGCAGGGTAGATAATCACTCACTGAGTGACATCAACATCATGGCGTCTCAGGGCACCAAACGATCTTATGAACAGATGGAAACTGGTGGAGAACGCCAGAATGCTACTGAGATCAGAGCATCTGTTGGAAGAATGGTTGGTGGAATTGGGAGGTTTTATATACAGATGTGCACTGAACTCAAACTCAGCGACTATGAAGGAAGGCTGATTCAGAACAGCATAACAATAGAGAGAATGGTTCTCTCTGCATTTGATGAAAGGAGGAACAAATACCTGGAAGAACATCCCAGTGCGGGGAAGGACCCAAAGAAAACTGGAGGTCCAATCTACCGAAGAAGAGACGGAAAATGGGTGAGAGAGCTGATTCTGTATGACAAAGAGGAGATCAGGAGAATTTGGCGTCAAGCGAACAATGGAGAAGATGCAACTGCTGGTCTCACTCACATGATGATCTGGCATTCCAATCTAAATGATGCCACATACCAGAGAACAAGAGCTCTCGTGCGTACTGGGATGGACCCTAGAATGTGCTCTCTGATGCAAGGATCAACTCTCCCGAGGAGATCTGGAGCTGCTGGTGCGGCAGTAAAGGGAGTCGGAACGATGGTGATGGAACTAATTCGGATGATAAAGCGAGGGATTAACGATCGGAATTTCTGGAGAGGTGAAAATGGGCGAAGAACAAGAATTGCATATGAGAGAATGTGCAACATCCTCAAAGGGAAATTCCAAACAGCAGCACAAAGAGCAATGATGGATCAGGTACGGGAAAGCAGAAATCCTGGGAATGCTGAGATTGAAGATCTCATATTTCTGGCACGGTCTGCACTCATCCTGAGAGGATCAGTGGCCCACAAGTCCTGCTTGCCTGCTTGTGTGTACGGGCTTGCCGTGGCCAGTGGATATGACTTTGAGAGAGAAGGGTACTCTCTGGTCGGGATTGATCCTTTCCGTCTGCTGCAAAACAGCCAGGTCTTTAGTCTAATTAGACCAAATGAGAATCCAGCACATAAAAGTCAATTGGTGTGGATGGCATGCCATTCTGCAGCATTTGAAGATCTGAGAGTCTCAAGCTTCATCAGAGGGACAAGAGTGGCCCCAAGGGGACAACTATCTACTAGAGGAGTTCAAATTGCTTCAAATGAGAACATGGAAACAATGGACTCCAGCACTCTTGAACTGAGAAGCAGATATTGGGCTATAAGGACCAGGAGTGGAGGAAACACCAACCAGCAGAGAGCATCTGCAGGACAAATCAGTGTGCAGCCTACTTTCTCGGTACAGAGAAATCTTCCCTTCGAAAGAGCGACCATTATGGCGGCATTCACAGGGAATACAGAGGGCAGAACATCTGACATGAGGACTGAAATCATAAGGATGATGGAAAGCTCCAGACCAGAAGATGTGTCTTTCCAGGGGCGGGGAGTCTTCGAGCTCTCGGACGAAAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAGTAATGAAGGATCTTATTTCTTCGGAGACAATGCAGAGGAATATGACAATTGAAGAAAAATACCCTTGTTTCTACT", + "description": "" + }, + "6": { + "name": "5787|A/Goose/Guangdong/1/96|EPI_ISL_1254|NA||", + "sequence": "AGCAAAAGCAGGAGATTAAAATGAATCCAAATCAGAAGATAATAACCATTGGATCAATCTGTATGGTAGTTGGGATAATTAGCTTGATGTTACAAATTGGGAACATAATCTCAATATGGGTCAGTCATTCAATTCAGACAGGGAATCAACACCAAGCTGAACCATGCAATCAAAGCATTATTACTTATGAAAACAACACCTGGGTAAATCAAACATATGTCAACATCAGCAATACCAATTTTCTTACTGAAAAAGCTGTGGCTTCAGTAACATTAGCGGGCAATTCATCTCTTTGCCCCATTAGCGGATGGGCTGTACACAGTAAGGACAACGGTATAAGAATCGGTTCCAAGGGGGATGTGTTTGTTATAAGAGAGCCGTTCATCTCATGCTCCCACTTGGAATGCAGAACTTTCTTTTTGACTCAGGGAGCCTTGCTGAATGACAAGCACTCCAATGGGACCGTCAAAGACAGAAGCCCTCACAGAACATTGATGAGTTGTCCTGTGGGTGAGGCTCCCTCCCCATATAACTCAAGGTTTGAGTCTGTTGCTTGGTCGGCAAGTGCTTGCCATGATGGCACCAGTTGGTTGACAATTGGAATTTCTGGCCCAGACAATGGGGCTGTGGCTGTATTGAAATACAACGGCATAATAACAGACACTATCAAGAGTTGGAGGAACAACATACTGAGAACTCAAGAGTCTGAATGTGCATGTGTAAATGGCTCTTGCTTTACTGTAATGACTGACGGACCAAGTAATGGGCAGGCCTCATATAAGATCTTCAAAATGGAAAAAGGGAAAGTAGTTAAATCAGTCGAATTGAATGCCCCTAATTATCACTATGAGGAGTGCTCCTGTTATCCTGATGCTGGCGAAATCACATGTGTGTGCAGGGATAATTGGCATGGCTCAAATCGGCCATGGGTATCTTTCAATCAAAATTTGGAGTATCAAATAGGATATATATGCAGTGGAGTTTTCGGAGACAATCCACGCCCCAATGATGGAACAGGCAGTTGTGGTCCGGTGTCCCCTAACGGGGCATATGGAGTAAAAGGGTTTTCATTTAAATACGGCAATGGTGTTTGGATCGGGAGAACCAAAAGCACTAATTCCAGGAGCGGCTTTGAAATGATTTGGGATCCAAATGGGTGGACTGGAACGGACAGTAGCTTCTCGGTGAAACAAGATATCGTAGCAATAACTGATTGGTCAGGATATAGCGGGAGTTTTGTCCAGCATCCAGAACTGACAGGATTAGATTGCATAAGACCTTGTTTCTGGGTTGAGCTAATCAGAGGGCGGCCCAAAGAGAGCACAATTTGGACTAGTGGGAGCAGCATATCTTTTTGTGGTGTAAATAGTGACACTGTGGGTTGGTCTTGGCCAGACGATGCCGAGTTGCCATTCACCATTGACAAGTAGTTTGTTCAAAAAACTCCTTGTTTCTACT", + "description": "" + }, + "7": { + "name": "5791|A/Goose/Guangdong/1/96|EPI_ISL_1254|MP||", + "sequence": "AGCAAAAGCAGGTAGATATTGAAAAATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCGTCCCGTCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAGGATGTCTTTGCAGGAAAGAACACCGATCTCGAGGCTCTCATGGAATGGCTAAAGACAAGACCAATCCTGTCACCTCTGACTAAAGGGATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAGAATGCCTTAAATGGAAATGGAGATCCAAACAATATGGATAGGGCAGTTAAGCTATACAAGAAGCTGAAAAGAGAAATAACATTCCATGGGGCTAAGGAGGTCGCACTCAGCTACTCAACCGGTGCACTTGCCAGTTGTATGGGTCTCATATACAACAGGATGGGAACGGTGACCACAGAAGTGGCTTTTGGCCTAGTGTGTGCCACTTGTGAGCAGATTGCAGATTCACAGCATCGGTCTCACAGACAGATGGCAACTACCACCAACCCACTAATCAGGCATGAGAACAGAATGGTGCTGGCCAGCACTACAGCTAAGGCTATGGAGCAGATGGCTGGATCGAGTGAGCAGGCAGCGGAAGCCATGGAGGTTGCTAGTCAGGCTAGGCAGATGGTGCAGGCAATGAGGACAATTGGGACTCATCCTAGCTCCAGTGCCGGTCTGAAAGATAATCTTCTTGAAAATTTGCAGGCCTACCAAAAACGAATGGGAGTGCAAATGCAGCGATTCAAGTGATCCTCTTGTTGTTGCCGCAAGTATCATTGGGATACTGCACTTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGGGTACCTGAGTCTATGAGGGAAGAGTATCGGCAGGAACAGCAGAGTGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAGCTGGAGTAAAAAACTACCTTGTTTCTACT", + "description": "" + }, + "8": { + "name": "5794|A/Goose/Guangdong/1/96|EPI_ISL_1254|NS||", + "sequence": "GTGACAAAGACATAATGGATTCCAACACGATAACCTCGTTTCAGGTAGATTGTTATCTATGGCACATAAGAAAGCTACTCAGTATGAGAGACATGTGTGATGCCCCCTTTGATGACAGGCTCCGAAGAGACCAAAAGGCATTAAAGGGAAGAGGCAGCACACTTGGACTCGATTTAAGAGTGGCTACAATGGAGGGGAAAAAGATCGTTGAGGACATCCTGAAGAGTGAGACAAATGAAAACCTCAAAATAGCCATTGCTTCCAGTCCTGCTCCTCGGTATATCACCGATATGAGCATAGAGGAGATGAGCCGAGAATGGTACATGCTGATGCCTAGGCAGAAAATAACTGGAGGCCTTATGGTGAAAATGGACCAAGCCATAATGGATAAAAGAATTATCCTTAAAGCAAATTTCTCAGTTCTATTTGATCAACTAGAGACATTAGTCTCTCTGAGGGCATTCACAGAAAGTGGTGCTATTGTGGCTGAAATATTTCCCATTCCCTCCGTACCAGGACATTTTACAGAGGATGTCAAAAATGCAATTGGAATCCTCATCGGTGGACTTGAATGGAATGATAACTCAATTCGAGCGTCTGAAAATATACAGAGATTCGCTTGGGGAATCCATGATGAGAATGGGGGACCTTCACTCCCTCCAAAACAGAAACGCTACATGGCGAAACGAGTTGAGTCAGAAGTTTGAAGAGATCAGATGGCTCATTGCTGAATGTAGAAATATACTGACAAAGACTGAAAATAGCTTTGAACAGATAACATTTTTGCAAGCATTGCAACTCTTACTTGAAGTTGAGAGTGAGATAAGGACCTTCTCTTTTCAGCTTATTTAATACTAAAAAACAC", + "description": "" + } + }, + "description": "A/Goose/Guangdong/1/96 EPI_ISL_1254" + }, + "A-Shanghai-02-2013": { + "name": "A-Shanghai-02-2013", + "subtype": "H7NX", + "segments": { + "1": { + "name": "568646|A/Shanghai/02/2013|EPI_ISL_173625|PB2|passage_details:_E1|", + "sequence": "ATGGAAAGAATAAAAGAACTAAGAGATTTGATGTCACAGTCTCGCACTCGCGAGATACTGACAAAAACAACTGTGGACCATATGGCCATAATCAAGAAATATACATCAGGAAGACAGGAGAAGAATCCTGCCCTTAGGATGAAGTGGATGATGGCAATGAAATATCCAATTACGGCAGACAAAAGGATAATGGAGATGATCCCGGAAAGAAATGAGCAAGGTCAGACCCTTTGGAGCAAGACAAATGATGCTGGATCAGACAGAGTGATGGTGTCACCTCTGGCTGTGACGTGGTGGAACAGAAATGGACCAACGACAAGCACAGTCCATTATCCAAAGGTCTATAAAACCTATTTTGAAAAGGTCGAAAGGCTAAAACATGGAACCTTCGGCCCCGTTCACTTCAGAAACCAGGTTAAAATACGCCGCAGGGTCGACATAAACCCGGGCCATGCAGATCTTAGTGCTAAAGAAGCACAGGATGTCATCATGGAGGTCGTATTCCCAAACGAAGTTGGAGCCAGAATATTGACATCAGAGTCACAGTTAACGATTACCAAGGAAAAGAAGAAGGAGCTTCAGGACTGCAAAATTGCCCCTTTAATGGTGGCTTACATGTTGGAGAGAGAACTGGTTCGCAAAACAAGATTCCTACCAGTAGCTGGAGGGACAAGCAGCGTGTATATCGAGGTGTTGCATTTGACCCAAGGGACCTGCTGGGAGCAAATGTACACACCGGGAGGGGAAGTGAGAAATGATGATGTTGATCAGAGTTTAATTATTGCTGCTAGAAATATTGTTAGAAGAGCAACAGTATCAGCAGACCCGTTGGCTTCGCTTTTGGAGATGTGCCATAGTACACAGATTGGCGGGATTAGGATGGTTGACATCCTTAGACAAAACCCAACAGAAGAACAGGCTGTGGATATATGTAAGGCAGCAATGGGTCTAAGGATCAGTTCATCCTTCAGCTTTGGAGGTTTCACTTTCAAAAGGACAAGTGGGTCATCTGTCAAAAGGGAAGAAGAAGTGCTCACAGGCAACCTCCAAACATTGAAAATAAGAGTACATGAAGGATATGAGGAATTCACAATGGTCGGGCGAAGAGCAACAGCCATTCTAAGGAAAGCAACCAGAAGACTGATCCAACTGATAGTGAGTGGGAAAGACGAGCAATCAATCGCCGAGGCAATCATAGTGGCAATGGTATTCTCACAAGAGGATTGTATGATAAAGGCAGTGAGAGGTGATTTGAACTTTGTCAACAGAGCAAACCAGCGGCTAAATCCCATGCATCAACTCCTGAGGCATTTCCAAAAGGATGCAAAGGTCCTGTTTCAAAACTGGGGAATTGAACCCATTGACAATGTAATGGGGATGATCGGAATATTGCCTGACATGACCCCCAGCACAGAGATGTCATTGAGAGGAGTGAGAGTTAGTAAAATGGGAGTAGATGAATATTCCAGCACTGAGAGAGTGGTCGTGAGTATTGATCGTTTCTTGAGGGTCCGAGACCAGAGGGGAAACGTACTCCTGTCTCCTGAAGAGGTTAGTGAAACACAGGGAACAGAAAAGCTGACTATAACATATTCATCGTCCATGATGTGGGAGATCAATGGTCCGGAATCAGTGCTAGTTAACACATATCAATGGATCATTAGAAATTGGGAAAATGTAAAGATTCAATGGTCCCAAGATCCTACAATGCTATACAATAAGATGGAATTTGAACCCTTTCAATCCCTAGTGCCTAAAGCTGCCAGGGGCCAATATAGTGGGTTCGTGAGGGTTCTATTCCAACAGATGCGTGACGTACTGGGAACATTTGACACTGTCCAAATAATAAAGCTATTACCATTTGCAGCAGCCCCGCCGAAGCAGAGTAGGATGCAGTTCTCTTCTCTAACTGTGAATGTGAGGGGTTCCGGAATGAGAATAGTTGTGAGAGGCAATTCTCCTGTGTTCAACTACAACAAGGCAACCAAGAGGCTTACGGTGCTTGGAAAGGATGCAGGTGCATTGATGGAAGACCCCGATGAGGGAACAGCAGGAGTGGAATCTGCGGTATTGAGGGGATTTCTGATTCTGGGCAAAGAAGACAAAAGATATGGGCCAGCATTGAGCATCAACGAATTGAGCAATCTTGCGAAAGGAGAGAAGGCTAATGTGTTGATAGGGCAAGGAGACGTTGTGTTGGTGATGAAACGGAAACGGGACTCTAGCATACTTACTGACAGTCAGACAGCGACCAAAAGGATTCGGATGGCCATCAATTAA", + "description": "" + }, + "2": { + "name": "568704|A/Shanghai/02/2013|EPI_ISL_173625|PB1|passage_details:_E1|", + "sequence": "ATGGATGTCAATCCGACTTTACTTTTCTTGAAAGTGCCAGTGCAAAATGCTATAAGTACCACTTTCCCTTATACTGGAGACCCTCCATACAGCCATGGAACAGGAACAGGATACACCATGGACACAGTCAACAGAACACATAAATACTCAGAAAAAGGAAAGTGGACAACGAACACAGAGACTGGAGCACCCCAACTCAATCCAATTGATGGACCATTACCTGAGGACAACGAGCCGAGTGGGTATGCACAAACGGATTGTGTATTGGAAGCAATGGCTTTCCTTGAAGAATCTCACCCAGGGATCTTTGAAAACTCGTGTCTCGAAACGATGGAAATTGTTCAGCAAACAAGAGTGGATAAACTGACCCAAGGCCGCCAGACCTATGACTGGACGTTGAATAGAAATCAGCCGGCTGCTACCGCATTGGCCAACACTATAGAGGTATTCAGATCGAATGGCCTGACAGCCAATGAATCAGGAAGGTTGATCGATTTCCTCAAGGACGTGATGGATTCAATGGATAAGGAAGAAATGGAGATTACAACACATTTCCAGAGGAAGAGGAGAGTGAGGGACAACATGACCAAGAAAATGGTCACACAGAGAACAATAGGAAAGAAAAAACAAAGACTGAACAAAAGGAGCTACCTAATAAGAGCACTTACATTGAACACAATGACAAAGGATGCTGAAAGAGGCAAGCTGAAAAGGAGGGCAATCGCAACACCCGGGATGCAAATCAGAGGATTCGTGTATTTTGTAGAAGCACTAGCGAGGAGCATCTGTGAGAAACTTGAGCAATCTGGCCTCCCTGTCGGAGGGAATGAGAAGAAAGCTAAATTGGCAAATGTTGTGAGGAAGATGATGACTAATTCACAAGATACAGAGCTCTCCTTCACAATTACTGGGGACAACACCAAATGGAATGAGAATCAAAACCCCCGGATGTTTCTAGCAATGATAACATACATCACAAGAAACCAGCCAGAATGGTTTAGAAATGTCTTAAGCATTGCTCCTATAATGTTCTCAAACAAGATGGCGAGATTAGGAAAAGGGTACATGTTCGAAAGTAAGAGTATGAAGTTACGGACACAAGTACCAGCGGAAATGCTCGCAAATATTGACCTGAAATACTTCAACAAATCAACAAGAGAGAAAATCGAGAAAATAAGACCTCTACTGATAGATGGCACAGCCTCATTGAGTCCTGGAATGATGATGGGCATGTTCAACATGTTGAGTACAGTCTTAGGAGTTTCAATTCTGAATCTCGGGCAGAAGAAGTACACCAAAACCACATATTGGTGGGACGGACTCCAATCCTCAGATGACTTCGCCCTCATAGTGAATGCACCGAATCATGAGGGAATACAGGCAGGAGTAGATAGGTTCTATAGAACCTGCAAATTAGTTGGGATAAACATGAGCAAGAAGAAATCCTACATAAATCGGACAGGAACATTCGAATTCACAAGCTTTTTCTACCGCTATGGATTCGTAGCTAACTTCAGTATGGAGTTGCCCAGTTTTGGAGTGTCCGGGATTAATGAGTCAGCTGACATGAGCGTTGGTGTTACAGTAATAAAGAACAATATGATAAACAACGATCTTGGACCAGCAACAGCCCAAATGGCCCTTCAGCTATTTATCAAAGACTACAGATACACATACCGATGTCACAGGGGTGATACGCAAATTCAAACGAGGAGAGCATTCGAGCTGAAGAAGCTGTGGGAGCAGACCCGTTCGAAGGCAGGACTGTTGGTTTCAGATGGAGGGCCAAACCTGTACAATATCCGGAACCTCCACATTCCAGAGGTCTGCTTGAAATGGGAATTGATGGATGAAGACTACCAAGGCAGGTTGTGTAATCCTATGAACCCGTTTGTCAGTCATAAGGAAATTGATTCAGTCAACAATGCTGTGGTGATGCCAGCTCATGGCCCAGCCAAAAGCATGGAGTATGATGCCGTTGCAACCACACATTCATGGATTCCTAAGAGGAATCGCTCCATTCTCAACACCAGCCAAAGGGGGATTCTTGAGGACGAACAGATGTACCAGAAGTGCTGCAACCTATTCGAAAAGTTCTTCCCCAGCAGTTCGTACAGGAGGCCAGTTGGAATTTCCAGCATGGTGGAGGCCATGGTGTCTAGGGCCCGAATTGATGCACGAATTGACTTCGAATCTGGAAGGATTAAGAAAGAAGAGTTTGCTGAGATCATGAAGATCTGTTCCACCATTGAAGAGCTCAGACGGCAAAAATAGTGAATTTAGCTTGTCCTTCATGA", + "description": "" + }, + "3": { + "name": "596649|A/Shanghai/02/2013|EPI_ISL_173625|PA|passage_details:_E1|", + "sequence": "ATGGAAGACTTTGTGCGACAGTGCTTCAATCCAATGATCGTCGAGCTTGCGGAAAAGGCAATGAAAGAATATGGGGAAGATCCGAAAATCGAAACAAACAAATTCGCATCAATATGCACACACTTAGAAGTCTGCTTCATGTACTCTGATTTCCACTTCATCGACGAACGAGGCGAATCAACTATAATAGAATCTGGCGATCCAAATGCGCTGCTGAAACACCGATTTGAAATAATCGAAGGGAGAGACCGAACAATGGCCTGGACAGTGGTGAATAGTATCTGCAACACCACAGGAGCCGAAAAACCCAAATTTCTCCCGGATCTGTATGACTACAAGGAAAACCGTTTCATTGAAATTGGAGTGACGAGGAGGGAAGTCCACATATATTACCTAGAGAAAGCCAATAAAATAAAATCCGAGAAGACACACATCCATATTTTTTCATTCACTGGAGAAGAGATGGCCACCAAAGCAGATTACACTCTTGACGAAGAAAGCAGGGCAAGAATCAAAACCAGGCTGTTCACCATAAGGCAGGAAATGGCCAGCAGGGGTCTATGGGATTCCTTTCGTCAGTCTGAAAGAGGCGAAGAAACAATTGAAGAAAGATTTGAAATCACAGGAACCATGCGCAGGCTTGCCGACCAAAGTCTCCCACCGAACTTCTCCAGCCTTGAAAACTTTAGAGCCTATGTGGATGGATTCGAACCGAACGGCTGCATTGAGGGCAAGCTTTCTCAGATGTCAAAAGAAGTGAACGCCAGAATTGAGCCATTTCTAAGAACAACACCACGCCCTCTCAGATTGCCTAATGGGCCTCCCTGCTCTCAGCGGTCGAAATTCTTGCTGATGGATGCTCTGAAATTAAGCATTGAGGACCCGAGCCACGAAGGGGAGGGGATACCGCTATATGATGCGATCAAATGCATGAAAACGTTCTTCGGGTGGAAAGAGCCCAACATTATCAAACCACATGAGAAAGGCATAAACCCCAATTATCTCCTGACTTGGAAGCAGGTGCTAGCAGAACTTCAGGACATTGAAAATGAAGAGAAGATTCCAAGGACAAAGAACATGAAGAAAACAAGCCAATTAAAGTGGGCACTCGGTGAGAACATGGCACCGGAGAAGGTGGACTTTGAGGATTGCAAAGATGTCAACGACTTGAAACAGTACAACAGTGATGAGCCAGAGCCCAGATCACTAGCATGTTGGATCCAGAATGAATTCAACAAGGCGTGTGAACTGACTGACTCAAGCTGGGTAGAACTTGATGAAATAGGGGAAGATGTTGCCCCAATCGAACACATTGCAAGCATGAGACGGAACTATTTTACAGCAGAGGTGTCCCACTGCAGGGCTACTGAATATATAATGAAGGGAGTGTACATAAATACAGCTTTGCTCAATGCATCTTGTGCAGCCATGGATGACTTTCAACTGATTCCAATGATAAGTAAATGTAGAACCAAAGAAGGAAGACGGAAAACAAACCTGTATGGATTCATTATAAAAGGAAGATCTCATTTGAGGAATGATACCGACGTGGTAAACTTTGTAAGTATGGAATTTTCCCTTACCGACCCAAGGTTGGAACCACATAAATGGGAAAAGTATTGTGTTCTTGAAATAGGGGACATGCTCCTGCGAACTGCAGTAGGCCAAGTGTCAAGACCCATGTTTCTGTATGTGAGAACCAATGGGACCTCCAAGATCAAGATGAAATGGGGTATGGAAATGAGACGCTGCCTTCTTCAATCTCTCCAACAGATTGAGAGCATGATTGAAGCTGAATCCTCCGTCAAAGAGAAAGACCTGACCAAAGAATTCTTTGAAAACAAATCAGAAACATGGCCAATTGGAGAGTCACCTAAAGGAGTGGAGGAAGGTTCCATCGGGAAGGTGTGCAGAACCTTACTAGCAAAATCTGTATTCAACAGCCTATATGCATCTCCGCAACTCGAGGGGTTCTCAGCTGAATCGAGAAAACTGCTACTCATTGTTCAGGCGCTTAGGGATAACCTGGAACCTGGAACCTTTGATCTTGAAGGGCTATATGAAGCAATCGAGGAGTGCCTGATTAATGATCCCTGGGTTTTGCTTAATGCATCTTGGTTCAACTCCTTCCTCACACATGCACTAAGATAGTTGTGGCAATGCTACTATTTGCTAT", + "description": "" + }, + "4": { + "name": "568648|A/Shanghai/02/2013|EPI_ISL_173625|HA|passage_details:_E1|", + "sequence": "ATGAACACTCAAATCCTGGTATTCGCTCTGATTGCGATCATTCCAACAAATGCAGACAAAATCTGCCTCGGACATCATGCCGTGTCAAACGGAACCAAAGTAAACACATTAACTGAAAGAGGAGTGGAAGTCGTCAATGCAACTGAAACAGTGGAACGAACAAACATCCCCAGGATCTGCTCAAAAGGGAAAAGGACAGTTGACCTCGGTCAATGTGGACTCCTGGGGACAATCACTGGACCACCTCAATGTGACCAATTCCTAGAATTTTCAGCCGATTTAATTATTGAGAGGCGAGAAGGAAGTGATGTCTGTTATCCTGGGAAATTCGTGAATGAAGAAGCTCTGAGGCAAATTCTCAGAGAATCAGGCGGAATTGACAAGGAAGCAATGGGATTCACATACAGTGGAATAAGAACTAATGGAGCAACCAGTGCATGTAGGAGATCAGGATCTTCATTCTATGCAGAAATGAAATGGCTCCTGTCAAACACAGATAATGCTGCATTCCCGCAGATGACTAAGTCATATAAAAATACAAGAAAAAGCCCAGCTCTAATAGTATGGGGGATCCATCATTCCGTATCAACTGCAGAGCAAACCAAGCTATATGGGAGTGGAAACAAACTGGTGACAGTTGGGAGTTCTAATTATCAACAATCTTTTGTACCGAGTCCAGGAGCGAGACCACAAGTTAATGGTCTATCTGGAAGAATTGACTTTCATTGGCTAATGCTAAATCCCAATGATACAGTCACTTTCAGTTTCAATGGGGCTTTCATAGCTCCAGACCGTGCAAGCTTCCTGAGAGGAAAATCTATGGGAATCCAGAGTGGAGTACAGGTTGATGCCAATTGTGAAGGGGACTGCTATCATAGTGGAGGGACAATAATAAGTAACTTGCCATTTCAGAACATAGATAGCAGGGCAGTTGGAAAATGTCCGAGATATGTTAAGCAAAGGAGTCTGCTGCTAGCAACAGGGATGAAGAATGTTCCTGAGATTCCAAAAGGAAGAGGCCTATTTGGTGCTATAGCGGGTTTCATTGAAAATGGATGGGAAGGCCTAATTGATGGTTGGTATGGTTTCAGACACCAGAATGCACAGGGAGAGGGAACTGCTGCAGATTACAAAAGCACTCAATCGGCAATTGATCAAATAACAGGAAAATTAAACCGGCTTATAGAAAAAACCAACCAACAATTTGAGTTGATAGACAATGAATTCAATGAGGTAGAGAAGCAAATCGGTAATGTGATAAATTGGACCAGAGATTCTATAACAGAAGTGTGGTCATACAATGCTGAACTCTTGGTAGCAATGGAGAACCAGCATACAATTGATCTGGCTGATTCAGAAATGGACAAACTGTACGAACGAGTGAAAAGACAGCTGAGAGAGAATGCTGAAGAAGATGGCACTGGTTGCTTTGAAATATTTCACAAGTGTGATGATGACTGTATGGCCAGTATTAGAAATAACACCTATGATCACAGCAAATACAGGGAAGAGGCAATGCAAAATAGAATACAGATTGACCCAGTCAAACTAAGCAGCGGCTACAAAGATGTGATACTTTGGTTTAGCTTCGGGGCATCATGTTTCATACTTCTAGCCATTGTAATGGGCCTTGTCTTCATATGTGTAAAGAATGGAAACATGCGGTGCACTATTTGTATATAAGTTTGGAAAAAACACCCTTGTTTCT", + "description": "" + }, + "5": { + "name": "568649|A/Shanghai/02/2013|EPI_ISL_173625|NP|passage_details:_E1|", + "sequence": "ATGGCGTCTCAAGGCACCAAACGATCCTATGAACAGATGGAAACTGGTGGGGAACGCCAGAATGCTACTGAGATCAGGGCATCTGTTGGAAGAATGGTTAGCGGCATTGGGAGATTCTACATACAGATGTGTACAGAACTCAAACTCAGTGACAATGAAGGGAGGCTGATTCAGAACAGTATAACAATAGAGAGAATGGTACTCTCTGCATTTGATGAAAGAAGGAACAGATACCTGGAAGAGCACCCCAGTGCAGGAAAGGACCCTAAGAAAACTGGAGGTCCAATTTACAGGAGAAGAGACGGAAAATGGGTGAGAGAGCTGATCCTGTATGACAAAGAGGAAATCAGGAGAATTTGGCGACAAGCGAACAATGGAGAGGATGCAACTGCTGGTCTTACCCATCTGATGATATGGCATTCCAACCTGAATGATGCTACCTATCAGAGAACGAGAGCTCTCGTGCGTACTGGAATGGATCCCCGGATGTGCTCTCTGATGCAAGGATCAACTCTCCCGAGGAGATCTGGAGCTGCAGGTGCAGCAGTGAAGGGGATAGGGACAATGGTGATGGAACTGATTCGGATGATAAAACGAGGGATCAACGACCGGAATTTCTGGAGAGGCGAAAATGGAAGAAGGACAAGAATTGCATATGAGAGAATGTGCAACATCCTCAAAGGGAAATTCCAAACAGCAGCACAAAGGGCAATGATGGATCAAGTGCGAGAGAGCAGAAATCCTGGGAATGCTGAAATAGAAGATCTCATTTTTCTGGCAAGGTCTGCACTCATCCTGAGAGGATCAGTGGCTCATAAATCCTGCTTGCCTGCTTGTGTGTACGGACTTGCAGTGGCTAGTGGATATGACTTTGAGAGAGAAGGGTACTCCTTGGTTGGAATAGATCCTTTCCGTCTGCTTCAAAACAGCCAGGTCTTTAGTCTCATTAGACCAAATGAGAACCCAGCACATAAGAGCCAACTAGTGTGGATGGCATGCCACTCTGCAGCGTTTGAGGACCTTAGGGTCTCAAGTTTCATTAGAGGGACAAGAATGGTCCCAAGAGGACAGCTATCCACTAGAGGGGTTCAAATTGCTTCAAATGAGAACATGGAAGCAATGGACTCCAATACTCTTGAACTGAGAAGTAGATATTGGGCTATAAGAACCAGAAGCGGAGGGAACACCAACCAACAGAGGGCATCTGCAGGACAGGTCAGCGTTCAACCCACTTTCTCAGTACAGAGAAACCTTCCTTTCGAAAGAGCAACCATTATGGCAGCATTTACAGGAAATACTGAGGGTAGAACGTCTGACATGAGGACTGAAATCATAAGAATGATGGAAAGTGCCAGACCAGAAGATGTGTCATTCCAGGGGCGGGGAGTCTTCGAGCTCTCGGACGAAAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAATAATGAAGGATCTTATTTCTTCGGAGACAATGCAGAGGAGTATGACAATTGAAGAAAAAAA", + "description": "" + }, + "6": { + "name": "568652|A/Shanghai/02/2013|EPI_ISL_173625|NA|passage_details:_E1|", + "sequence": "ATGAATCCAAATCAGAAGATTCTATGCACTTCAGCCACTGCTATCATAATAGGCGCAATCGCAGTACTCATTGGAATGGCAAACCTAGGATTGAACATAGGACTGCATCTAAAACCGGGCTGCAATTGCTCACACTCACAACCTGAAACAACCAACACAAGCCAAACAATAATAAACAACTATTATAATGAAACAAACATCACCAAYATCCAAATGGAAGAGAGAACAAGCAGGAATTTCAATAACTTAACTAAAGGGCTCTGTACTATAAATTCATGGCACATATATGGGAAAGACAATGCAGTAAGAATTGGAGAGAGCTCGGATGTTTTAGTCACAAGAGAACCCTATGTTTCATGCGACCCAGATGAATGCAGGTTCTATGCTCTCAGCCAAGGAACAACAATCAGAGGGAAACACTCAAACGGAACAATACACGATAGGTCCCAGTATCGCGCCCTGATAAGCTGGCCACTATCATCACCGCCCACAGTGTACAACAGCAGGGTGGAATGCATTGGGTGGTCAAGTACTAGTTGCCATGATGGCAAATCCAGGATGTCAATATGTATATCAGGACCAAACAACAATGCATCTGCAGTAGTATGGTACAACAGAAGGCCTGTTGCAGAAATTAACACATGGGCCCGAAACATACTAAGAACACAGGAATCTGAATGTGTATGCCACAACGGCGTATGCCCAGTAGTGTTCACCGATGGGTCTGCCACTGGACCTGCAGACACAAGAATATACTATTTTAAAGAGGGGAAAATATTGAAATGGGAGTCTCTGACTGGAACTGCTAAGCATATTGAAGAATGCTCATGTTACGGGGAACGAACAGGAATTACCTGCACATGCAGGGACAATTGGCAGGGCTCAAATAGACCAGTGATTCAGATAGACCCAGTAGCAATGACACACACTAGTCAATATATATGCAGTCCTGTTCTTACAGACAATCCCCGACCGAATGACCCAAATATAGGTAAGTGTAATGACCCTTATCCAGGTAATAATAACAATGGAGTCAAGGGATTCTCATACCTGGATGGGGCTAACACTTGGCTAGGGAGGACAATAAGCACAGCCTCGAGGTCTGGATACGAGATGTTAAAAGTGCCAAATGCATTGACAGATGATAGATCAAAGCCCATTCAAGGTCAGACAATTGTATTAAACGCTGACTGGAGTGGTTACAGTGGATCTTTCATGGACTATTGGGCTGAAGGGGACTGCTATCGAGCGTGTTTTTATGTGGAGTTGATACGTGGAAGACCCAAGGAGGATAAAGTGTGGTGGACCAGCAATAGTATAGTATCGATGTGTTCCAGTACAGAATTCCTGGGACAATGGAACTGGCCTGATGGGGCTAAAATAGAGTACTTCCTCTAA", + "description": "" + }, + "7": { + "name": "568650|A/Shanghai/02/2013|EPI_ISL_173625|MP|passage_details:_E1|", + "sequence": "ATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATTCCATCAGGCCCCCTCAAAGCCGAGATCGCACAGAGACTTGAGGATGTTTTTGCAGGGAAGAACGCAGATCTCGAGGCTCTCATGGAGTGGATAAAGACAAGACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCCTAAATGGGAATGGAGACCCAAACAACATGGACAAGGCGGTTAAATTATACAAGAAACTGAAGAGGGAAATGACATTTCATGGAGCAAAGGAAGTTGCACTCAGTTACTCAACTGGTGCGCTTGCCAGCTGCATGGGTCTCATATACAACAGAATGGGGACTGTGACCGCAGAAGGGGCTCTTGGACTAGTATGTGCCACTTGTGAGCAGATTGCTGACGCACAACATCGGTCCCACAGGCAGATGGCGACTACTACTAACCCACTAATTAGGCATGAGAATAGAATGGTACTAGCCAGCACTACGGCTAAGGCTATGGAGCAGATGGCTGGATCAAGTGAACAGGCAGCGGAAGCCATGGAAGTTGCAAGTCAGGCTAGGCAAATGGTGCAGGCTATGAGAACAGTTGGGACTCACCCTAACTCCAGTACAGGTCTAAAAGATGATCTTATTGAAAATTTGCAGGCCTACCAGAACCGGATGGGAGTGCAACTGCAGCGGTTCAAGTGAGCCTCTAGTCGTTGCAGCTAACATTATTGGGATATTGCACTTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGTTTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGAATGCCTGAGTCTATGAGGGAAGAATATCGGCAGGAACAGCAGAATGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAGCTGAAGTAAAAA", + "description": "" + }, + "8": { + "name": "568651|A/Shanghai/02/2013|EPI_ISL_173625|NS|passage_details:_E1|", + "sequence": "ATGGATTCCAATACTGTGTCAAGCTTCCAGGTAGACTGCTTTCTTTGGCATGTCCGCAAACGATTTGCAGACCAAGAAATGGGTGATGCCCCATTTCTAGACCGGCTTCGCCGAGATCAGAAGTCCCTGAGAGGAAGAAGCAGCACTCTTGGTCTGGACATCAGAACTGCCACGCGTGAAGGAAAGCATATAGTGGAGCGGATTTTAGAGGAAGAGTCAGATGAAGCATTTAAAATGAGTATTGCTTCAGTGCCAGCTCCACGCTATCTAACTGACATGACTCTTGAAGAAATGTCAAGAGATTGGTTAATGCTCATTCCCAAACAGAAAATAACAGGGTCCCTATGCATTAGAATGGACCAAGCAATAGTGGACAAAAACATCACATTGAAAGCAAATTTCAGTGTGATTTTCAATCGGCTTGAAGCCCTGATACTACTTAGAGCTTTTACGGAAGAAGGAGCAATTGTAGGCGAAATCTCACCATTACCTTCTCTTCCAGGACATACTGACAAGGATGTCAAAAATGCAATTGAGATCCTCATCGGAGGATTTGAATGGAATGATAACACAGTTCGAGTCTCTGAAACTCTACAGAGATTCGCTTGGAGAAGCAGCGATGAGGATGGGAGATCTCCACTCTCTACAAAGTAGAAACGGGAAATGGAGAGAACAGTTAAGCCAGAAGTTCGAAGAAATAAGATGGTTGATTGAAGAAGTACGACATAGATTAAAAATTACGGAGAATAGCTTTGAGCAAATAACTTTTATGCAAGCCTTACAACTATTGCTTGAAGTGGAGCAAGAGATAAGAACTTTCTCGTTTCAGCTTATTTAATGA", + "description": "" + } + }, + "description": "A/Shanghai/02/2013 EPI_ISL_173625" + }, + "A-Hong-Kong-1073-99": { + "name": "A-Hong-Kong-1073-99", + "subtype": "H9NX", + "segments": { + "1": { + "name": "12032|A/Hong_Kong/1073/99|EPI_ISL_140|PB2||", + "sequence": "GCCAAAAGCAGGTCAATTATATTCAATATGGAAAGAATAAAAGAACTAAGAAATTTGATGTCGCAATCTCGCACTCGCGAGATACTGACAAAAACCACTGTGGATCATATGGCCATAATTAAGAAGTACACATCAGGAAGACAGGAGAAGAATCCCGCTCTTAGAATGAAATGGATGATGGCGATGAAATACCCGATCACAGCTGACAAAAGAATAATGGAGATGATCCCTGAAAGGAATGAGCAAGGCCAAACTCTTTGGAGCAAAACAAATGACGCTGGATCAGACAGGGTAATGGTATCACCTCTGGCTGTAACGTGGTGGAACAGAAATGGACCAACAACAAGTACAGTCCATTATCCAAAGGTGTATAAAACCTACTTTGAAAAGGTTGAAAGATTAAAACACGGAACCTTTGGCCCTGTTCATTTCCGGAATCAAGTCAAAATACGCCGCAGGGTTGACATGAACCCTGGCCATGCAGATCTCAGCGCTAAAGAAGCACAAGATGTCATCATGGAGGTCGTTTTCCCAAATGAAGTTGGAGCCAGGATATTGACATCAGAATCACAGCTGACAATAACAAAGGAAAAGAGGGAGGAACTCAAGAATTGTAATATTGCTCCTTTAATGGTGGCATATATGTTGGAAAGAGAATTGGTTCGCAAGACCAGATTCCTACCCGTGGCTGGCGGGACAAGCAGCGTATATATAGAAGTATTGCATTTGACTCAAGGAACTTGCTGGGAGCAGATGTACACACCAGGAGGGGAGGTAAGAAATGATGATGTTGACCAAAGTTTAATCATTGCTGCTAGGAACATTGTCAGGAGAGCAACAGTATCAGCAGACCCATTGGCTTCACTCCTGGAAATGTGCCATAGCACACAAATTGGCGGAGTAAGAATGGTAGACATCCTTAAACAAAACCCAACAGAAGAGCAAGCTGTAGATATATGCAAGGCAGCAATGGGTTTGAAAATCAGCTCATCCTTCAGCTTTGGAGGGTTCACTTTCAAAAGAACAAAGGGGTCTTCTGTCAAAAGAGAGGAAGAAGTGCTTACAGGCAACCTCCAAACATTGAAGATAAAAGTACATGAAGGATATGAGGAATTCACAATGGTTGGACGAAGAGCAACAGCCATTCTAAGAAAAGCAACCAGAAGGATGATCCAACTGATAGTCAGCGGAAGGGACGAGCAATCAATTGCTGAGGCAATTATTGTGGCAATGGTGTTCTCACAAGAAGATTGCATGGTAAAGGCAGTCCGAGGTGATTTGAATTTCGTAAACAGAGCAAATCAACGACTGAATCCCATGCACCAACTCCTGAGACACTTTCAAAAGGATGCAAAGGTGCTGTTTCAAAACTGGGGAATTGAACCCATCGACAATGTCATGGGTATGATTGGAATATTGCCTGACATGACCCCCAGCACGGAAATGTCACTAAGAGGAGTGAGAGTTAGCAAAATGGGGGTGGATGAATATTCTAGCACTGAAAGGGTGGTCGTGAGCATTGACCGTTTCTTAAGGGTCCGAGATCAGCGAGGAAATGTACTCCTATCCCCTGAAGAAGTTAGTGAAACACAGGGAATGGAAAAGTTGACGATAACTTATTCATCGTCTATGATGTGGGAGATTAACGGGCCAGAATCAGTGCTAGTTAACACATATCAATGGATCATTAGGAATTGGGAGACTGTAAAGATCCAATGGTCCCAAGAACCCACCATGCTATACAATAAGATGGAGTTTGAACCATTTCAATCTTTAGTACCAAAGGCTGCCAGAAGCCAATATAGTGGATTTGTGAGAACGCTATTCCAGCAGATGCGTGATGTTTTGGGAACGTTCGACACTGTTCAAATAATCAAACTACTACCATTTGCAGCAGCCCCACCGGAACAGAGTAGGATGCAATTTTCTTCTCTGACTGTGAATGTGAGGGGATCAGGAATGAGAATACTTGTGAGAGGTAACTCCCCTGCATTTAACTACAACAAGACAACTAAGAGGCTTACAATACTTGGGAAGGACGCAGGTGCGCTTACAGAGGACCCAGATGAAGGAACAGCAGGAGTAGAGTCTGCAGTATTGAGAGGATTTCTAATCCTCGGCAAAGAAGACAAAAGATATGGACCAGCATTAAGCATCAATGAACTGAGCAATCTTACGAAAGGGGAGAAAGCTAATGTATTGATAGGGCAAGGAGACGTAGTGTTGGTAATGAAACGGAAACGGGACTCTAGCATACTTACTGACAGCCAGACAGCGACCAAAAGAATTCGGATGGCCATCAATTAGTGTCGAATTGTTTAAAAACGACCTTGTTTCTACT", + "description": "" + }, + "2": { + "name": "12039|A/Hong_Kong/1073/99|EPI_ISL_140|PB1||", + "sequence": "GCAAAAGCAGGCAAACCATTTGAATGGATGTCAATCCGACTTTACTTTTCTTAAAAGTGCCAGCGCAAAATGCAATAAGTACCACATTCCCTTATACTGGAGATCCCCCATATAGCCATGGAACAGGAACAGGATACACCATGGACACAGTCAACAGAACACATCAATATTCAGAAAAAGGGAGGTGGACAACAAACACAGAGACCGGAGCACCCCAACTCAACCCTATTGATGGACCATTACCTGAAGACAATGAGCCGAGCGGGTATGCACAAACAGATTGTGTATTGGAAGCAATGGCTTTCCTTGAAGAATCCCACCCAGGACTCTTTGAAAACTCATGTCTTGAAACGATGGAAGTTGTCCAGCAAACGAGAGTGGATAAGCTGACCCAAGGTCGCCAGACTTATGACTGGACATTGAATAGAAACCAGCCGGCTGCAACTGCTTTGGCCAACACCATAGAAGTATTCAGATCGAACGGTCTAACAGCCAATGAGTCAGGAAGGTTAATAGATTTCCTCAAGGACGTAATGGAATCAATGGATAAGGAAGAAATGGAAATAACAACACATTTCCAGAGAAAGAGAAGAGTGAGGGACAACATGACCAAGAAAATGGTCACACAAAGAACAATAGGGAAGAAGAAGCAAAAGCTGACAAAAAAGAGCTACCTAATAAGAGCACTGACACTGAACACAATGACAAAAGATGCTGAAAGGGGAAAATTGAAAAGACGAGCGATTGCAACACCCGGAATGCAAATCAGAGGATTCGTGCACTTTGTCGAAGCACTAGCAAGGAGCATCTGTGAAAAACTTGAGCAATCTGGACTCCCCGTTGGAGGGAATGAGAAGAAGGCTAAATTGGCAAATGTTGTGAGAAAGATGATGACTAACTCACAAGACACAGAGCTCTCCTTTACAGTTACCGGAGACAACACCAAATGGAATGAGAATCAGAATCCTCGAATATTTCTAGCAATGATAACATACATCACAAGGAACCAACCTGAATGGTTTAGAAATGTCTTGAGCATTGCCCCTATAATGTTCTCAAATAAAATGGCGAGGTTAGGAAAAGGATACATGTTCGAGAGTAAGAGCATGAAGCTACGGACACAAATACCAGCAGAAATGCTTGCAAACATTGACTTGAAATACTTCAACGAATCGACGAGAAAGAAAATTGAGAAAATAAGACCTCTACTAATAGAGGGCACAGCCTCATTGAGTCCAGGGATGATGATGGGCATGTTTAATATGCTAAGTACGGTCTTAGGAGTCTCAATCTTAAATCTTGGGCAGAAGAGGTACACCAAAACCACATACTGGTGGGATGGGCTCCAATCCTCTGATGATTTCGCTCTCATAGTGAATGCACCAAATCATGAGGGAATACAAGCAGGAGTGGATAGATTCTATAGGACTTGCAAGCTAGTTGGAATCAACATGAGCAAAAAGAAGTCTTACATAAATCGGACAGGAACATTTGAGTTCACAAGCTTTTTCTACCGCTATGGGTTTGTAGCCAACTTCAGCATGGAGCTGCCCAGCTTTGGAGTTTCCGGAATTAATGAATCGGCTGACATGAGCATTGGAGTTACAGTGATAAAGAATAATATGATAAACAACGACCTTGGACCAGCAACAGCCCAGATGGCTCTTCAGCTGTTCATTAAAGACTACAGATACACCTACCGATGCCACAGAGGTGATACACAAATTCAAACTAGAAGATCATTTGAATTGAAGAAGCTGTGGGAGCAGACCCGCTCAAAGGCAGGACTGTTGGTTTCAGATGGAGGGCCGAATTTATACAACATCCGGAATCTTCACATTCCAGAAGTTTGCTTGAAGTGGGAGTTGATGGATGAAGATTACCAGGGAAGACTGTGTAACCCTCTGAACCCGTTTGTCAGTCATAAGGAAGTTGAATCCGTCAACAATGCTGTGGTAATGCCAGCCCATGGTCCGGCCAAGAGCATGGAATATGATGCCGTTGCAACTACACATTCATGGATTCCCAAGAGAAATCGCTCCATTCTCAACACTAGCCAAAGGGGAATTCTTGAGGATGAACAAATGTACCAGAAGTGCTGCACTCTATTCGAGAAATTCTTCCCTAGCAGTTCATATCGGAGGCCAGTTGGAATTTCCAGCATGATGGAGGCCATGGTGTCTAGGGCCCGAATTGATGCACGGATTGACTTCGAGTCTGGAAGGATTAAGAAAGAAGAATTTGCTGAGATCTTGAAGATCTGTTCCACCATTGAAGAGCTCGGACGGCAAGGGAAGTGAATTTGGCTTGTCCTTCATGAAAAAATGC", + "description": "" + }, + "3": { + "name": "12042|A/Hong_Kong/1073/99|EPI_ISL_140|PA||", + "sequence": "AAAGCAGGTACTGATCCAAAATGGAAGACTTTGTGCGACAGTGCTTCAATCCAATGATTGTCGAGCTTGCGGAAAAGACAATGAAGGAATATGGGGAAGACCCGAAAATTGAAACAAATAAGTTCGCTGCAATATGCACACACTTAGAAGTCTGCTTCATGTATTCAGACTTCCATTTCATTGACGAACGAGGCGAATCAATAATTGTGGAATCTGGTGATCCAAATGCATTGTTGAAGCACAGGTTTGAAATAATTGAAGGAAGAGACCGAGCAATGGCCTGGACAGTGGTGAATAGCATCTGCAACACAACAGGAGTCGATAAACCCAAATTTCTTCCGGATCTATACGACTACAAGGAAAACCGATTCACTGAAATTGGTGTGACACGGAGGGAAGTTCACATATATTACTTAGAAAAAGCTAACAAGATAAAATCCGAGAAAACACATATCCACATCTTTTCATTCACTGGAGAAGAAATGGCCACTAAAGCTGACTACACCCTTGATGAAGAGAGCAGGGCAAGAATAAAAACCAGACTATTCACCATAAGACAGGAAATGGCAAGCAGGGGTCTATGGGATTCCTTTCGTCAGTCCGAGAGAGGCGAAGAGACAATTGAAGAAAGATTTGAAATCACAGGGACCATGCGTAGGCTTGCCGACCAAAGTCTCCCACCTAACTTCTCCAGCCTTGAAAACTTTAGAGCCTATGTGGATGGATTCAAACCGAACGGCTGCATTGAGGGCAAGCTTTCTCAAATGTCGAAAGAAGTGAACGCCAGAATTGAGCCATTTCTGAAGACAACACCACGTCCCCTCAGATTGCCTGATGGACCTCCCTGCTCCCAGCGGTCGAAATTCTTGCTGATGGATGCTCTGAAATTAAGCATTGAGGACCCGAGCCATGAGGGGGAGGGGATACCGCTATATGATGCGATAAAATGCATGAAAACATTCTTCGGCTGGAGAGAGCCCAACATCATCAAGCCACACGAGAAGGGCATAAATCCCAATTATCTTCTGGCTTGGAAGCAGGTGCTGGCAGAACTCCAGGATATTGAAAATGAGGATAAAATCCCAAAAACAAAGAACATGAAGAAAACAAGCCAATTAATGTGGGCACTCGGGGAGAATATGGCACCGGAAAAATTGGACTTTGAGGACTGCAAAGATATTGGCGATCTGAAACAGTATCAAAGTGATGAGCCAGAGCTCAGATCGATAGCAAGCTGGATCCAGAGTGAGTTCAACAAGGCATGTGAATTGACCGATTCGAGCTGGATAGAACTCGATGAGATAGGGGAAGATGTTGCCCCAATTGAGCACATTGCAAGCATGAGAAGGAACTACTTCACAGCGGAAGTGTCTCATTGCAGGGCCACTGAGTACATAATGAAGGGGGTTTACATAAATACAGCTTTGCTCAATGCATCTTGTGCAGCCATGGATGACTTCCAACTGATTCCAATGATAAGCAAATGCAGAACAAAAGAAGGAAGAAGGAAGACAAACCTGTATGGGTTCATTATAAAAGGAAGGTCCCATTTGAGAAATGATACTGACGTGGTGAACTTTGTGAGTATGGAATTCTCCCTTACTGACCCAAGGCTGGAGCCACACAAATGGGAAAAGTACTGTGTTCTTGAAGTAGGGGAAATGCTCTTGCGGACTGCAATAGGCCAGGTGTCAAGGCCCATGTTCCTGTATGTGAGAACTAACGGAACCTCCAAAATTAAGATGAAATGGGGGATGGAAATGAGACGCTGCCTTCTTCAATCTCTTCAACAGATTGAGAGCATGATCGAGGCTGAGTCTTCTATCAAAGAGAAAGACATGACCAAAGAATTCTTTGAAAACAGATCGGAGACATGGCCAATTGGAGAGTCACCTAAGGGAGTGGAGGAAGGCTCAATCGGGAAGGTGTGCAGAACCTTACTAGCAAAATCTGTGTTCAACAGCCTATATTCATCTCCACAACTCGAAGGATTTTCAGCTGAATCGAGAAAACTACTACTCATTGTTCAAGCACTTAGGGACAACCTGGAACCTGGAACCTTTGATCTTGAAGGGCTATATGGAGCAATTGAGGAGTGCCTGATTAATGATCCCTGGGTTTTGCTTAATGCATCTTGGTTCAACTCCTTCCTCACACATGCACTAAAATAGTTGTGGCAATGCTACTATTTGCTATCCATACTGTCCAAAAAAGTACCTTGTTTC", + "description": "" + }, + "4": { + "name": "12024|A/Hong_Kong/1073/99|EPI_ISL_140|HA||", + "sequence": "GCAAAAGCAGGGGAATTACTTAACTAGCAAAATGGAAACAATATCACTAATAACTATACTACTAGTAGTAACAGCAAGCAATGCAGATAAAATCTGCATCGGCCACCAGTCAACAAACTCCACAGAAACTGTGGACACGCTAACAGAAACCAATGTTCCTGTGACACATGCCAAAGAATTGCTCCACACAGAGCATAATGGAATGCTGTGTGCAACAAGCCTGGGACATCCCCTCATTCTAGACACATGCACTATTGAAGGACTAGTCTATGGCAACCCTTCTTGTGACCTGCTGTTGGGAGGAAGAGAATGGTCCTACATCGTCGAAAGATCATCAGCTGTAAATGGAACGTGTTACCCTGGGAATGTAGAAAACCTAGAGGAACTCAGGACACTTTTTAGTTCCGCTAGTTCCTACCAAAGAATCCAAATCTTCCCAGACACAACCTGGAATGTGACTTACACTGGAACAAGCAGAGCATGTTCAGGTTCATTCTACAGGAGTATGAGATGGCTGACTCAAAAGAGCGGTTTTTACCCTGTTCAAGACGCCCAATACACAAATAACAGGGGAAAGAGCATTCTTTTCGTGTGGGGCATACATCACCCACCCACCTATACCGAGCAAACAAATTTGTACATAAGAAACGACACAACAACAAGCGTGACAACAGAAGATTTGAATAGGACCTTCAAACCAGTGATAGGGCCAAGGCCCCTTGTCAATGGTCTGCAGGGAAGAATTGATTATTATTGGTCGGTACTAAAACCAGGCCAAACATTGCGAGTACGATCCAATGGGAATCTAATTGCTCCATGGTATGGACACGTTCTTTCAGGAGGGAGCCATGGAAGAATCCTGAAGACTGATTTAAAAGGTGGTAATTGTGTAGTGCAATGTCAGACTGAAAAAGGTGGCTTAAACAGTACATTGCCATTCCACAATATCAGTAAATATGCATTTGGAACCTGCCCCAAATATGTAAGAGTTAATAGTCTCAAACTGGCAGTCGGTCTGAGGAACGTGCCTGCTAGATCAAGTAGAGGACTATTTGGAGCCATAGCTGGATTCATAGAAGGAGGTTGGCCAGGACTAGTCGCTGGCTGGTATGGTTTCCAGCATTCAAATGATCAAGGGGTTGGTATGGCTGCAGATAGGGATTCAACTCAAAAGGCAATTGATAAAATAACATCCAAGGTGAATAATATAGTCGACAAGATGAACAAGCAATATGAAATAATTGATCATGAATTCAGTGAGGTTGAAACTAGACTCAATATGATCAATAATAAGATTGATGACCAAATACAAGACGTATGGGCATATAATGCAGAATTGCTAGTACTACTTGAAAATCAAAAAACACTCGATGAGCATGATGCGAACGTGAACAATCTATATAACAAGGTGAAGAGGGCACTGGGCTCCAATGCTATGGAAGATGGGAAAGGCTGTTTCGAGCTATACCATAAATGTGATGATCAGTGCATGGAAACAATTCGGAACGGGACCTATAATAGGAGAAAGTATAGAGAGGAATCAAGACTAGAAAGGCAGAAAATAGAGGGGGTTAAGCTGGAATCTGAGGGAACTTACAAAATCCTCACCATTTATTCGACTGTCGCCTCATCTCTTGTGCTTGCAATGGGGTTTGCTGCCTTCCTGTTCTGGGCCATGTCCAATGGATCTTGCAGATGCAACATTTGTATATAA", + "description": "" + }, + "5": { + "name": "11567|A/Hong_Kong/1073/99|EPI_ISL_140|NP||", + "sequence": "AGCAGGGTTAATAATCACTCACTGAGTGACATCAACATCATGGCGTCGCAAGGCACCAAACGATCCTATGAACAGATGGAAACTGGTGGAGAACGCCAGAATGCCACTGAGATCAGGGCATCTGTTGGAAGAATGGTTGGTGGAATTGGGAGGTTTTACGTACAGATGTGCACTGAACTCAAACTCAGCGACCAAGAAGGAAGGTTGATCCAGAACAGTATAACAATAGAGAGAATGGTTCTCTCCGCATTTGATGAAAGGAGGAACAGGTACCTAGAGGAACATCCCAGTGCGGGGAAGGACCCGAAGAAGACCGGAGGTCCAATCTACCGAAGGAGAGACGGGAAATGGGTGAGAGAGCTGATTCTGTATGACAAAGAGGAGATAAGGAGAATTTGGCGTCAAGCGAACAATGGAGAAGACGCAACTGCTGGTCTCACTCATATGATGATCTGGCATTCCAACCTAAATGATGCCACATACCAGAGAACAAGAGCCCTCGTGCGGACTGGAATGGACCCCAGAATGTGCTCTCTGATGCAAGGATCAACCCTCCCGAGGAGATCTGGAGCTGCTGGTGCAGCAATAAAGGGAGTCGGGACAATGGTAATGGAACTAATTCGGATGATAAAGCGAGGCATTAATGACCGGAACTTCTGGAGAGGCGATAATGGACGAAGAACAAGGATTGCATATGAGAGAATGTGCAACATCCTCAAAGGGAAATTTCAAACAGCAGCACAAAGAGCAATGATGGATCAGGTGCGAGAAAGCAGAAATCCTGGGAATGCTGAAATTGAAGATCTCATCTTTCTGGCACGGTCTGCACTCATCCTGAGAGGATCCGTAGCCCATAAGTCCTGCTTGCCTGCTTGTGTGTACGGGCTCGCTGTGGCCAGTGGATATGATTTTGAGAGGGAAGGGTACTCTCTGGTTGGGATAGATCCTTTCCGTCTGCTTCAGAACAGTCAGGTCTTCAGTCTTATTAGACCAAATGAGAATCCAGCACATAAAAGTCAATTGGTATGGATGGCATGCCATTCTGCAGCATTTGAGGACCTGAGAGTCTCAAGTTTCATTAGAGGAACAAGAGTGATCCCAAGAGGACAACTATCCACTAGAGGAGTTCAGATTGCTTCAAATGAGAACGTGGAAGCAATGGATTCCAGCACTCTTGAACTGAGAAGCAGATATTGGGCTATAAGGACCAGGAGTGGAGGAAACACCAATCAACAGAGAGCATCTGCAGGACAAATCAGTGTACAGCCCACTTTCTCAGTACAGAGAAATCTTCCCTTCGAAAGACCGACCATTATGGCTGCGTTTAAGGGGAATACCGAGGGCAGAACATCTGACATGAGGACTGAAATCATAAGGATGATGGAAAGTGCCAGACCAGAAGATGTGTCTTTCCAGGGGCGGGGAGTCTTCGAGCTCTCGGACGAAAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAGTAATGAAGGATCTTATTTCTTCGGAGACAATGCAGAGGAATATGACAATTGAGGAAAAATACCCTTGTTTCTA", + "description": "" + }, + "6": { + "name": "12030|A/Hong_Kong/1073/99|EPI_ISL_140|NA||", + "sequence": "ATGAATCCAAATCAAAAGATAATAGCACTTGGCTCTGTTTCTATAACTATTGCGACAATATGTTTACTCATGCAGATTGCCATCTTAGCAACGACTATGACACTACATTTCAATGAATGTACCAACCCATCGAACAATCAAGCAGTGCCATGTGAACCAATCATAATAGAAAGGAACATAACAGAGATAGTGCATTTGAATAATACTACCATAGAGAAGGAAAGTTGTCCTAAAGTAGCAGAATACAAGAATTGGTCAAAACCGCAATGTCAAATTACAGGGTTCGCCCCTTTCTCCAAGGACAACTCAATTAGGCTTTCTGCAGGCGGGGATATTTGGGTGACAAGAGAACCTTATGTATCGTGCGGTCTTGGTAAATGTTACCAATTTGCACTTGGGCAGGGAACCACTTTGAACAACAAACACTCAAATGGCACAATACATGATAGGAGTCCCCATAGAACCCTTTTAATGAACGAGTTGGGTGTTCCATTTCATTTGGGAACCAAACAAGTGTGCATAGCATGGTCCAGCTCAAGCTGCCATGATGGGAAGGCATGGTTACATGTTTGTGTCACTGGGGATGATAGAAATGCGACTGCTAGCATCATTTATGATGGGATGCTTACCGACAGTATTGGTTCATGGTCTAAGAACATCCTCAGAACTCAGGAGTCAGAATGCGTTTGCATCAATGGAACTTGTACAGTAGTAATGACTGATGGAAGTGCATCAGGAAGGGCTGATACTAAAATACTATTCATTAGAGAAGGGAAAATTGTCCACATTGGTCCACTGTCAGGAAGTGCTCAGCATGTGGAGGAATGCTCCTGTTACCCCCGGTATCCAGAAGTTAGATGTGTTTGCAGAGACAATTGGAAGGGCTCCAATAGACCCGTGCTATATATAAATGTGGCAGATTATAGTGTTGATTCTAGTTATGTGTGCTCAGGACTTGTTGGCGACACACCAAGAAATGACGATAGCTCCAGCAGCAGTAACTGCAGGGATCCTAATAACGAGAGAGGGGGCCCAGGAGTGAAAGGGTGGGCCTTTGACAATGGAAATGATGTTTGGATGGGACGAACAATCAAGAAAGATTCGCGCTCTGGTTATGAGACTTTCAGGGTCGTTGGTGGTTGGACTACGGCTAATTCCAAGTCACAAATAAATAGGCAAGTCATAGTTGACAGTGATAACTGGTCTGGGTATTCTGGTATATTCTCTGTTGAAGGAAAAACCTGCATCAACAGGTGTTTTTATGTGGAGTTGATAAGAGGGAGACCACAGGAGACCAGAGTATGGTGGACTTCAAATAGCATCATTGTATTTTGTGGAACTTCAGGTACCTATGGAACAGGCTCATGGCCTGATGGAGCGAATATCAATTTCATGTCTATATAAGCTTTCGCAATTTT", + "description": "" + }, + "7": { + "name": "11556|A/Hong_Kong/1073/99|EPI_ISL_140|MP||", + "sequence": "GGGGAATTCCAAAAGCAGGTAGATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATCCCATCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAGGATGTTTTTGCAGGGAAGAACACAGATCTTGAGGCTCTCATGGAATGGCTAAAGACAAGACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGATTTGTCCAAAATGCCCTAAATGGGAATGGAGACCCAAACAACATGGACAGGGCAGTTAAACTATACAAGAAGCTGAAGAGGGAAATGACATTCCATGGAGCAAAGGAAGTTGCACTCAGTTACTCAACTGGTGCGCTTGCCAGTTGCATGGGTCTCATATACAACCGGATGGGAACAGTGACCACAGAAGTGGCTCTTGGCCTAGTATGTGCCACTTGTGAACAGATTGCTGATGCCCAACATCGGTCCCACAGGCAGATGGCGACTACCACCAACCCACTAATCAGGCATGAGAACAGAATGGTACTAGCCAGCACTACGGCTAAGGCCATGGAGCAGATGGCTGGATCAAGTGAGCAGGCAGCAGAAGCCATGGAAGTCGCAAGTCAGGCTAGGCAAATGGTGCAGGCTATGAGGACAATTGGGACTCACCCTAGTTCCAGTGCAGGTCTAAAAGATGATCTTATTGAAAATTTGCAGGCTTACCAGAAACGGATGGGAGTGCAAATGCAGAGATTCAAGTGATCCTCTCGTTGTTGCAGCAAGTATCATTGGGATATTGCACTTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGCTTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGAGTGCCTGAGTCTATGAGGGAAGAGTATCGGCAGGAACAGCAGAATGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAGCTGGAGTAAAAGATCTTCCT", + "description": "" + }, + "8": { + "name": "11562|A/Hong_Kong/1073/99|EPI_ISL_140|NS||", + "sequence": "AGCAAAAGCAGGGTGACAAAGACATAATGGATTCCAACACTGTGTCAAGCTTTCAGGTAGACTGCTTTCTTTGGCATGTCCGCAAACGATTTGCAGACCAAGAACTGGGTGATGCCCCATTCCTTGACCGGCTTCGCCGAGATCAGAAGTCCCTAAGAGGAAGAGGCAGCACTCTTGGTCTGGACATCAGAACTGCCACTCGTGAAGGAAAGCATATAGTGGAGCGGATTCTGGAGGAAGAATCTGACGAGGCACTTAAAATGACTATCGCTTCAGTGCCTGCTTCACGCTACCTAACTGAAATGACTCTTGAGGAAATGTCAAGGGATTGGTTAATGCTCATTCCCAAGCAGAAAGTGACAGGGCCCCTTTGCATTAGAATGGACCAGGCAGTAATGGGTAAAACCATCATATTGAAAGCAAACTTTAGTGTGATTTTTAATCGACTTGAAGCTCTGATACTACTTAGAGCGTTTACAGATGAAGGAGCAATAGTGGGCGAAATCTCACCATTACCTTCCCTTCCAGGACATACTGACGAGGATGTCAAAAATGCAATTGGGGTCCTCATCGGAGGACTTGAATGGAATGATAACACAGTTCGAGTCTCTGAAACTCTACAGAGATTCACTTGGAGAAGCAGTGATGAGAATGGGAGATCTCCACTCCCTCCAAAACAGAAACGGAAAGTGGAGAGAACAATTGAGCCAGAAGTTTGAAGAGATAAGATGGTTAATTGAAGAAATGCGACATAGGTTAAGAATTACAGAGAATAGCTTTGAGCAAATAACCTTTATGCAAGCCTTACAACTATTGCTTGAAGTGGAGCAAGAGATAAGAACTTTCTCGTTTCAGCTTATTTAATGATAAAAAACACCCTTGTTTCTACT", + "description": "" + } + }, + "description": "" } } \ No newline at end of file diff --git a/workflow_flu_gisaid_ingest/Snakefile b/workflow_flu_gisaid_ingest/Snakefile index d4da7775..68a3cf84 100644 --- a/workflow_flu_gisaid_ingest/Snakefile +++ b/workflow_flu_gisaid_ingest/Snakefile @@ -1,5 +1,9 @@ # coding: utf-8 +"""GISAID ingestion for Flu PathMut +$ snakemake -j6 +""" + import datetime import os import gzip @@ -26,10 +30,10 @@ rule all: # Find input chunks METADATA_CHUNKS, = glob_wildcards(os.path.join( - data_folder, "metadata", "{metadata_chunk}.xls" + data_folder, "raw_data", "{metadata_chunk}.xls" )) SEQUENCE_CHUNKS, = glob_wildcards(os.path.join( - data_folder, "sequences", "{sequence_chunk}.fasta" + data_folder, "raw_data", "{sequence_chunk}.fasta" )) rule clean_metadata: @@ -37,7 +41,7 @@ rule clean_metadata: """ input: metadata_chunks = expand( - os.path.join(data_folder, "metadata", "{metadata_chunk}.xls"), + os.path.join(data_folder, "raw_data", "{metadata_chunk}.xls"), metadata_chunk=METADATA_CHUNKS ) output: @@ -62,7 +66,7 @@ checkpoint chunk_sequences: """ input: sequences = expand( - os.path.join(data_folder, "sequences", "{sequence_chunk}.fasta"), + os.path.join(data_folder, "raw_data", "{sequence_chunk}.fasta"), sequence_chunk=SEQUENCE_CHUNKS ), metadata = rules.clean_metadata.output.metadata_clean diff --git a/workflow_flu_gisaid_ingest/scripts/clean_metadata.py b/workflow_flu_gisaid_ingest/scripts/clean_metadata.py index 07668af3..7e7a37ba 100755 --- a/workflow_flu_gisaid_ingest/scripts/clean_metadata.py +++ b/workflow_flu_gisaid_ingest/scripts/clean_metadata.py @@ -137,6 +137,14 @@ def clean_df(df): df.loc[~b_serotype, "serotype"] = ( df.loc[~b_serotype, "serotype"].str.split("/").apply(lambda x: x[1]).str.strip() ) + # Generalize H5, H7, H9, H10 serotypes + # But first save the original serotype + df["original_serotype"] = df["serotype"] + df.loc[df["serotype"].str.startswith("H5"), "serotype"] = "H5NX" + df.loc[df["serotype"].str.startswith("H7"), "serotype"] = "H7NX" + # df['serotype'].str.replace(r'^H7N?[1-9]?$', 'H7NX', regex=True) + df.loc[df["serotype"].str.startswith("H9"), "serotype"] = "H9NX" + df.loc[df["serotype"].str.startswith("H10"), "serotype"] = "H10NX" # Remove rows without segments df = df.loc[df["segments"].apply(len) > 0, :] diff --git a/workflow_main/analyses/Snakefile b/workflow_main/analyses/Snakefile index 15ade2b6..367f3437 100644 --- a/workflow_main/analyses/Snakefile +++ b/workflow_main/analyses/Snakefile @@ -142,6 +142,7 @@ rule global_seq_data: isolate_data = os.path.join(data_folder, "isolate_data.csv"), metadata_map = os.path.join(data_folder, "metadata_map.json") params: + min_date = config['min_date'], out_folder = os.path.join(data_folder, "new_global_data") output: case_count = os.path.join(data_folder, "new_global_data", "case_count.json"), @@ -153,6 +154,7 @@ rule global_seq_data: python3 analyses/scripts/global_seq_data.py \ --isolate-data {input.isolate_data} \ --metadata-map {input.metadata_map} \ + --min-date {params.min_date} \ --output {params.out_folder} """ diff --git a/workflow_main/analyses/scripts/global_seq_data.py b/workflow_main/analyses/scripts/global_seq_data.py index 13697d20..3f66c6af 100644 --- a/workflow_main/analyses/scripts/global_seq_data.py +++ b/workflow_main/analyses/scripts/global_seq_data.py @@ -23,6 +23,9 @@ def main(): parser.add_argument( "--metadata-map", type=str, required=True, help="Metadata map JSON file" ) + parser.add_argument( + "--min-date", type=str, required=True, help="Minimum date for data" + ) parser.add_argument( "-o", "--output", type=str, required=True, help="Path to output directory", ) @@ -190,7 +193,7 @@ def rename_countries(country): # Only take dates from 2019-12-15 isolate_df = isolate_df.loc[ - isolate_df["collection_date"] > pd.to_datetime("2019-12-15") + isolate_df["collection_date"] > pd.to_datetime(args.min_date) ] # Calculate time deltas