From ef806a5d873424e20e5a4baaf607e2e6b4aaddca Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Mon, 13 Nov 2023 15:16:14 -0800 Subject: [PATCH] Use genbank_accession column as ID column --- Snakefile | 16 +++++++-- config/config_zika.yaml | 2 ++ example_data/metadata.tsv | 70 ++++++++++++++++++------------------ example_data/sequences.fasta | 68 +++++++++++++++++------------------ 4 files changed, 84 insertions(+), 72 deletions(-) create mode 100644 config/config_zika.yaml diff --git a/Snakefile b/Snakefile index 3562078..4f7dbfe 100644 --- a/Snakefile +++ b/Snakefile @@ -1,3 +1,6 @@ +if not config: + configfile: "config/config_zika.yaml" + rule all: input: auspice_json = "auspice/zika.json", @@ -59,12 +62,14 @@ rule filter: group_by = "country year month", sequences_per_group = 40, min_date = 2012, - min_length = 5385 + min_length = 5385, + strain_id = config.get("strain_id_field", "strain"), shell: """ augur filter \ --sequences {input.sequences} \ --metadata {input.metadata} \ + --metadata-id-columns {params.strain_id} \ --exclude {input.exclude} \ --output {output.sequences} \ --group-by {params.group_by} \ @@ -124,13 +129,15 @@ rule refine: params: coalescent = "opt", date_inference = "marginal", - clock_filter_iqd = 4 + clock_filter_iqd = 4, + strain_id = config.get("strain_id_field", "strain"), shell: """ augur refine \ --tree {input.tree} \ --alignment {input.alignment} \ --metadata {input.metadata} \ + --metadata-id-columns {params.strain_id} \ --output-tree {output.tree} \ --output-node-data {output.node_data} \ --timetree \ @@ -212,12 +219,15 @@ rule export: auspice_config = files.auspice_config, description = files.description output: - auspice_json = rules.all.input.auspice_json + auspice_json = rules.all.input.auspice_json, + params: + strain_id = config.get("strain_id_field", "strain"), shell: """ augur export v2 \ --tree {input.tree} \ --metadata {input.metadata} \ + --metadata-id-columns {params.strain_id} \ --node-data {input.branch_lengths} {input.traits} {input.nt_muts} {input.aa_muts} \ --colors {input.colors} \ --auspice-config {input.auspice_config} \ diff --git a/config/config_zika.yaml b/config/config_zika.yaml new file mode 100644 index 0000000..5345584 --- /dev/null +++ b/config/config_zika.yaml @@ -0,0 +1,2 @@ +strain_id_field: "genbank_accession" +display_strain_field: "strain" \ No newline at end of file diff --git a/example_data/metadata.tsv b/example_data/metadata.tsv index 9c30f2e..6e5345c 100644 --- a/example_data/metadata.tsv +++ b/example_data/metadata.tsv @@ -1,35 +1,35 @@ -strain virus accession date region country division city db segment authors url title journal paper_url -PAN/CDC_259359_V1_V3/2015 zika KX156774 2015-12-18 North America Panama Panama Panama genbank genome Shabman et al https://www.ncbi.nlm.nih.gov/nuccore/KX156774 Direct Submission Submitted (29-APR-2016) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA https://www.ncbi.nlm.nih.gov/pubmed/ -COL/FLR_00024/2015 zika MF574569 2015-12-XX South America Colombia Colombia Colombia genbank genome Pickett et al https://www.ncbi.nlm.nih.gov/nuccore/MF574569 Direct Submission Submitted (28-JUL-2017) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA https://www.ncbi.nlm.nih.gov/pubmed/ -PRVABC59 zika KU501215 2015-12-XX North America Puerto Rico Puerto Rico Puerto Rico genbank genome Lanciotti et al https://www.ncbi.nlm.nih.gov/nuccore/KU501215 Phylogeny of Zika Virus in Western Hemisphere, 2015 Emerging Infect. Dis. 22 (5), 933-935 (2016) https://www.ncbi.nlm.nih.gov/pubmed/27088323 -COL/FLR_00008/2015 zika MF574562 2015-12-XX South America Colombia Colombia Colombia genbank genome Pickett et al https://www.ncbi.nlm.nih.gov/nuccore/MF574562 Direct Submission Submitted (28-JUL-2017) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA https://www.ncbi.nlm.nih.gov/pubmed/ -Colombia/2016/ZC204Se zika KY317939 2016-01-06 South America Colombia Colombia Colombia genbank genome Quick et al https://www.ncbi.nlm.nih.gov/nuccore/KY317939 Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples Nat Protoc 12 (6), 1261-1276 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28538739 -ZKC2/2016 zika KX253996 2016-02-16 Oceania American Samoa American Samoa American Samoa genbank genome Wu et al https://www.ncbi.nlm.nih.gov/nuccore/KX253996 Direct Submission Submitted (18-MAY-2016) Center for Diseases Control and Prevention of Guangdong Province; National Institute of Viral Disease Control and Prevention, China https://www.ncbi.nlm.nih.gov/pubmed/ -VEN/UF_1/2016 zika KX702400 2016-03-25 South America Venezuela Venezuela Venezuela genbank genome Blohm et al https://www.ncbi.nlm.nih.gov/nuccore/KX702400 Complete Genome Sequences of Identical Zika virus Isolates in a Nursing Mother and Her Infant Genome Announc 5 (17), e00231-17 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28450510 -DOM/2016/BB_0059 zika KY785425 2016-04-04 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785425 Zika virus evolution and spread in the Americas Nature 546 (7658), 411-415 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28538734 -BRA/2016/FC_6706 zika KY785433 2016-04-08 South America Brazil Brazil Brazil genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785433 Zika virus evolution and spread in the Americas Nature 546 (7658), 411-415 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28538734 -DOM/2016/BB_0183 zika KY785420 2016-04-18 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785420 Zika virus evolution and spread in the Americas Nature 546 (7658), 411-415 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28538734 -EcEs062_16 zika KX879603 2016-04-XX South America Ecuador Ecuador Ecuador genbank genome Marquez et al https://www.ncbi.nlm.nih.gov/nuccore/KX879603 First Complete Genome Sequences of Zika Virus Isolated from Febrile Patient Sera in Ecuador Genome Announc 5 (8), e01673-16 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28232448 -HND/2016/HU_ME59 zika KY785418 2016-05-13 North America Honduras Honduras Honduras genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785418 Zika virus evolution and spread in the Americas Nature 546 (7658), 411-415 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28538734 -DOM/2016/MA_WGS16_011 zika KY785484 2016-06-06 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785484 Zika virus evolution and spread in the Americas Nature 546 (7658), 411-415 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28538734 -DOM/2016/BB_0433 zika KY785441 2016-06-13 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785441 Zika virus evolution and spread in the Americas Nature 546 (7658), 411-415 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28538734 -USA/2016/FL022 zika KY075935 2016-07-22 North America Usa Usa Usa genbank genome Grubaugh et al https://www.ncbi.nlm.nih.gov/nuccore/KY075935 Genomic epidemiology reveals multiple introductions of Zika virus into the United States Nature (2017) In press https://www.ncbi.nlm.nih.gov/pubmed/28538723 -SG_027 zika KY241697 2016-08-27 Southeast Asia Singapore Singapore Singapore genbank genome Ho et al https://www.ncbi.nlm.nih.gov/nuccore/KY241697 Outbreak of Zika virus infection in Singapore: an epidemiological, entomological, virological, and clinical analysis Lancet Infect Dis (2017) In press https://www.ncbi.nlm.nih.gov/pubmed/ -SG_074 zika KY241744 2016-08-28 Southeast Asia Singapore Singapore Singapore genbank genome Ho et al https://www.ncbi.nlm.nih.gov/nuccore/KY241744 Outbreak of Zika virus infection in Singapore: an epidemiological, entomological, virological, and clinical analysis Lancet Infect Dis (2017) In press https://www.ncbi.nlm.nih.gov/pubmed/ -SG_056 zika KY241726 2016-08-28 Southeast Asia Singapore Singapore Singapore genbank genome Ho et al https://www.ncbi.nlm.nih.gov/nuccore/KY241726 Outbreak of Zika virus infection in Singapore: an epidemiological, entomological, virological, and clinical analysis Lancet Infect Dis (2017) In press https://www.ncbi.nlm.nih.gov/pubmed/ -USA/2016/FLUR022 zika KY325473 2016-08-31 North America Usa Usa Usa genbank genome Grubaugh et al https://www.ncbi.nlm.nih.gov/nuccore/KY325473 Genomic epidemiology reveals multiple introductions of Zika virus into the United States Nature (2017) In press https://www.ncbi.nlm.nih.gov/pubmed/28538723 -Aedes_aegypti/USA/2016/FL05 zika KY075937 2016-09-09 North America Usa Usa Usa genbank genome Grubaugh et al https://www.ncbi.nlm.nih.gov/nuccore/KY075937 Genomic epidemiology reveals multiple introductions of Zika virus into the United States Nature (2017) In press https://www.ncbi.nlm.nih.gov/pubmed/28538723 -SG_018 zika KY241688 2016-09-13 Southeast Asia Singapore Singapore Singapore genbank genome Ho et al https://www.ncbi.nlm.nih.gov/nuccore/KY241688 Outbreak of Zika virus infection in Singapore: an epidemiological, entomological, virological, and clinical analysis Lancet Infect Dis (2017) In press https://www.ncbi.nlm.nih.gov/pubmed/ -USA/2016/FLWB042 zika KY325478 2016-09-26 North America Usa Usa Usa genbank genome Grubaugh et al https://www.ncbi.nlm.nih.gov/nuccore/KY325478 Genomic epidemiology reveals multiple introductions of Zika virus into the United States Nature (2017) In press https://www.ncbi.nlm.nih.gov/pubmed/28538723 -COL/PRV_00028/2015 zika MF574578 2016-12-XX South America Colombia Colombia Colombia genbank genome Pickett et al https://www.ncbi.nlm.nih.gov/nuccore/MF574578 Direct Submission Submitted (30-JUL-2017) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA https://www.ncbi.nlm.nih.gov/pubmed/ -Thailand/1610acTw zika MF692778 2016-10-XX Southeast Asia Thailand Thailand Thailand genbank genome Lin et al https://www.ncbi.nlm.nih.gov/nuccore/MF692778 Imported Zika virus strains, Taiwan, 2016 Unpublished https://www.ncbi.nlm.nih.gov/pubmed/ -1_0087_PF zika KX447509 2013-12-XX Oceania French Polynesia French Polynesia French Polynesia genbank genome Pettersson et al https://www.ncbi.nlm.nih.gov/nuccore/KX447509 How Did Zika Virus Emerge in the Pacific Islands and Latin America? MBio 7 (5), e01239-16 (2016) https://www.ncbi.nlm.nih.gov/pubmed/27729507 -1_0199_PF zika KX447519 2013-11-XX Oceania French Polynesia French Polynesia French Polynesia genbank genome Pettersson et al https://www.ncbi.nlm.nih.gov/nuccore/KX447519 How Did Zika Virus Emerge in the Pacific Islands and Latin America? MBio 7 (5), e01239-16 (2016) https://www.ncbi.nlm.nih.gov/pubmed/27729507 -1_0181_PF zika KX447512 2013-12-XX Oceania French Polynesia French Polynesia French Polynesia genbank genome Pettersson et al https://www.ncbi.nlm.nih.gov/nuccore/KX447512 How Did Zika Virus Emerge in the Pacific Islands and Latin America? MBio 7 (5), e01239-16 (2016) https://www.ncbi.nlm.nih.gov/pubmed/27729507 -Brazil/2015/ZBRC301 zika KY558995 2015-05-13 South America Brazil Brazil Brazil genbank genome Faria et al https://www.ncbi.nlm.nih.gov/nuccore/KY558995 Epidemic establishment and cryptic transmission of Zika virus in Brazil and the Americas Unpublished https://www.ncbi.nlm.nih.gov/pubmed/ -Brazil/2015/ZBRA105 zika KY558989 2015-02-23 South America Brazil Brazil Brazil genbank genome Faria et al https://www.ncbi.nlm.nih.gov/nuccore/KY558989 Establishment and cryptic transmission of Zika virus in Brazil and the Americas Nature 546 (7658), 406-410 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28538727 -Brazil/2016/ZBRC16 zika KY558991 2016-01-19 South America Brazil Brazil Brazil genbank genome Faria et al https://www.ncbi.nlm.nih.gov/nuccore/KY558991 Epidemic establishment and cryptic transmission of Zika virus in Brazil and the Americas Unpublished https://www.ncbi.nlm.nih.gov/pubmed/ -V8375 zika KU501217 2015-11-01 North America Guatemala Guatemala Guatemala genbank genome Lanciotti et al https://www.ncbi.nlm.nih.gov/nuccore/KU501217 Phylogeny of Zika Virus in Western Hemisphere, 2015 Emerging Infect. Dis. 22 (5), 933-935 (2016) https://www.ncbi.nlm.nih.gov/pubmed/27088323 -Nica1_16 zika KX421195 2016-01-19 North America Nicaragua Nicaragua Nicaragua genbank genome Tabata et al https://www.ncbi.nlm.nih.gov/nuccore/KX421195 Zika Virus Targets Different Primary Human Placental Cells, Suggesting Two Routes for Vertical Transmission Cell Host Microbe 20 (2), 155-166 (2016) https://www.ncbi.nlm.nih.gov/pubmed/27443522 -Brazil/2015/ZBRC303 zika KY558997 2015-05-14 South America Brazil Brazil Brazil genbank genome Faria et al https://www.ncbi.nlm.nih.gov/nuccore/KY558997 Epidemic establishment and cryptic transmission of Zika virus in Brazil and the Americas Unpublished https://www.ncbi.nlm.nih.gov/pubmed/ -SMGC_1 zika KX266255 2016-02-14 Oceania American Samoa American Samoa American Samoa genbank genome Bi et al https://www.ncbi.nlm.nih.gov/nuccore/KX266255 Genetic and Biological Characterization for Zika Viruses Imported through Shenzhen Port Chin. Sci. Bull. 61 (22), 2463-2474 (2016) https://www.ncbi.nlm.nih.gov/pubmed/ +strain virus genbank_accession date region country division city db segment authors url +PAN/CDC_259359_V1_V3/2015 zika KX156774 2015-12-18 North America Panama Panama Panama genbank genome Shabman et al https://www.ncbi.nlm.nih.gov/nuccore/KX156774 +COL/FLR_00024/2015 zika MF574569 2015-12-XX South America Colombia Colombia Colombia genbank genome Pickett et al https://www.ncbi.nlm.nih.gov/nuccore/MF574569 +PRVABC59 zika KU501215 2015-12-XX North America Puerto Rico Puerto Rico Puerto Rico genbank genome Lanciotti et al https://www.ncbi.nlm.nih.gov/nuccore/KU501215 +COL/FLR_00008/2015 zika MF574562 2015-12-XX South America Colombia Colombia Colombia genbank genome Pickett et al https://www.ncbi.nlm.nih.gov/nuccore/MF574562 +Colombia/2016/ZC204Se zika KY317939 2016-01-06 South America Colombia Colombia Colombia genbank genome Quick et al https://www.ncbi.nlm.nih.gov/nuccore/KY317939 +ZKC2/2016 zika KX253996 2016-02-16 Oceania American Samoa American Samoa American Samoa genbank genome Wu et al https://www.ncbi.nlm.nih.gov/nuccore/KX253996 +VEN/UF_1/2016 zika KX702400 2016-03-25 South America Venezuela Venezuela Venezuela genbank genome Blohm et al https://www.ncbi.nlm.nih.gov/nuccore/KX702400 +DOM/2016/BB_0059 zika KY785425 2016-04-04 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785425 +BRA/2016/FC_6706 zika KY785433 2016-04-08 South America Brazil Brazil Brazil genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785433 +DOM/2016/BB_0183 zika KY785420 2016-04-18 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785420 +EcEs062_16 zika KX879603 2016-04-XX South America Ecuador Ecuador Ecuador genbank genome Marquez et al https://www.ncbi.nlm.nih.gov/nuccore/KX879603 +HND/2016/HU_ME59 zika KY785418 2016-05-13 North America Honduras Honduras Honduras genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785418 +DOM/2016/MA_WGS16_011 zika KY785484 2016-06-06 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785484 +DOM/2016/BB_0433 zika KY785441 2016-06-13 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785441 +USA/2016/FL022 zika KY075935 2016-07-22 North America Usa Usa Usa genbank genome Grubaugh et al https://www.ncbi.nlm.nih.gov/nuccore/KY075935 +SG_027 zika KY241697 2016-08-27 Southeast Asia Singapore Singapore Singapore genbank genome Ho et al https://www.ncbi.nlm.nih.gov/nuccore/KY241697 +SG_074 zika KY241744 2016-08-28 Southeast Asia Singapore Singapore Singapore genbank genome Ho et al https://www.ncbi.nlm.nih.gov/nuccore/KY241744 +SG_056 zika KY241726 2016-08-28 Southeast Asia Singapore Singapore Singapore genbank genome Ho et al https://www.ncbi.nlm.nih.gov/nuccore/KY241726 +USA/2016/FLUR022 zika KY325473 2016-08-31 North America Usa Usa Usa genbank genome Grubaugh et al https://www.ncbi.nlm.nih.gov/nuccore/KY325473 +Aedes_aegypti/USA/2016/FL05 zika KY075937 2016-09-09 North America Usa Usa Usa genbank genome Grubaugh et al https://www.ncbi.nlm.nih.gov/nuccore/KY075937 +SG_018 zika KY241688 2016-09-13 Southeast Asia Singapore Singapore Singapore genbank genome Ho et al https://www.ncbi.nlm.nih.gov/nuccore/KY241688 +USA/2016/FLWB042 zika KY325478 2016-09-26 North America Usa Usa Usa genbank genome Grubaugh et al https://www.ncbi.nlm.nih.gov/nuccore/KY325478 +COL/PRV_00028/2015 zika MF574578 2016-12-XX South America Colombia Colombia Colombia genbank genome Pickett et al https://www.ncbi.nlm.nih.gov/nuccore/MF574578 +Thailand/1610acTw zika MF692778 2016-10-XX Southeast Asia Thailand Thailand Thailand genbank genome Lin et al https://www.ncbi.nlm.nih.gov/nuccore/MF692778 +1_0087_PF zika KX447509 2013-12-XX Oceania French Polynesia French Polynesia French Polynesia genbank genome Pettersson et al https://www.ncbi.nlm.nih.gov/nuccore/KX447509 +1_0199_PF zika KX447519 2013-11-XX Oceania French Polynesia French Polynesia French Polynesia genbank genome Pettersson et al https://www.ncbi.nlm.nih.gov/nuccore/KX447519 +1_0181_PF zika KX447512 2013-12-XX Oceania French Polynesia French Polynesia French Polynesia genbank genome Pettersson et al https://www.ncbi.nlm.nih.gov/nuccore/KX447512 +Brazil/2015/ZBRC301 zika KY558995 2015-05-13 South America Brazil Brazil Brazil genbank genome Faria et al https://www.ncbi.nlm.nih.gov/nuccore/KY558995 +Brazil/2015/ZBRA105 zika KY558989 2015-02-23 South America Brazil Brazil Brazil genbank genome Faria et al https://www.ncbi.nlm.nih.gov/nuccore/KY558989 +Brazil/2016/ZBRC16 zika KY558991 2016-01-19 South America Brazil Brazil Brazil genbank genome Faria et al https://www.ncbi.nlm.nih.gov/nuccore/KY558991 +V8375 zika KU501217 2015-11-01 North America Guatemala Guatemala Guatemala genbank genome Lanciotti et al https://www.ncbi.nlm.nih.gov/nuccore/KU501217 +Nica1_16 zika KX421195 2016-01-19 North America Nicaragua Nicaragua Nicaragua genbank genome Tabata et al https://www.ncbi.nlm.nih.gov/nuccore/KX421195 +Brazil/2015/ZBRC303 zika KY558997 2015-05-14 South America Brazil Brazil Brazil genbank genome Faria et al https://www.ncbi.nlm.nih.gov/nuccore/KY558997 +SMGC_1 zika KX266255 2016-02-14 Oceania American Samoa American Samoa American Samoa genbank genome Bi et al https://www.ncbi.nlm.nih.gov/nuccore/KX266255 diff --git a/example_data/sequences.fasta b/example_data/sequences.fasta index 64facba..9203c90 100644 --- a/example_data/sequences.fasta +++ b/example_data/sequences.fasta @@ -1,4 +1,4 @@ ->PAN/CDC_259359_V1_V3/2015 +>KX156774 gaatttgaagcgaatgctaacaacagtatcaacaggttttattttggatttggaaacgag agtttctggtcatgaaaaacccaaaaaagaaatccggaggattccggattgtcaatatgc taaaacgcggagtagcccgtgtgagcccctttgggggcttgaagaggctgccagccggac @@ -179,7 +179,7 @@ gaccttccccacccttcaatctggggcctgaactggagatcagctgtggatctccagaag agggactagtggttagaggagaccccccggaaaacgcaaaacagcatattgacgctggga aagaccagagactccatgagtttccaccacgctggccgccaggcacagatcgccgaatag cggcggccggtgtggggaaatccatgggtct ->COL/FLR_00024/2015 +>MF574569 tcagactgcgacagttcgagtttgaagcgaaagctagcaacagtatcaacaggttttatt ttggatttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggaggatt ccggattgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaa @@ -358,7 +358,7 @@ agctgggaaaccaagcctatagtcaggccgagaacgccatggcacggaagaagccatgct gcctgtgagcccctcagaggacactgagtcaaaaaaccccacgcgcttggaggcgcagga tgggaaaagaaggtggcgaccttccccacccttcaatctggggcctgaactggagatcag ctgtggatctccagaagagggactagtggttagaggaga ->PRVABC59 +>KU501215 gttgttgatctgtgtgaatcagactgcgacagttcgagtttgaagcgaaagctagcaaca gtatcaacaggttttattttggatttggaaacgagagtttctggtcatgaaaaacccaaa aaagaaatccggaggattccggattgtcaatatgctaaaacgcggagtagcccgtgtgag @@ -537,7 +537,7 @@ tgtgacccccccaggagaagctgggaaaccaagcctatagtcaggccgagaacgccatgg cacggaagaagccatgctgcctgtgagcccctcagaggacactgagtcaaaaaaccccac gcgcttggaggcgcaggatgggaaaagaaggtggcgaccttccccacccttcaatctggg gcctgaactggagatcagctgtggatctccagaagagggactagtggttagagga ->COL/FLR_00008/2015 +>MF574562 tcagactgcgacagttcgagtttgaagcgaaagctagcaacagtatcaacaggttttatt ttggatttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggaggatt ccggattgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaa @@ -716,7 +716,7 @@ agctgggaaaccaagcctatagtcaggccgagaacgccatggcacggaagaagccatgct gcctgtgagcccctcagaggacactgagtcaaaaaaccccacgcgcttggaggcgcagga tgggaaaagaaggtggcgaccttccccacccttcaatctggggcctgaactggagatcag ctgtggatctccagaagagggactagtggttagaggaga ->Colombia/2016/ZC204Se +>KY317939 gacagttcgagtttgaagcgaaagctagcaacagtatcaacaggttttattttggatttg gaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggaggattccggattgt caatatgctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaagaggctgcc @@ -894,7 +894,7 @@ agtcagccacagcttggggaaagctgtgcagcctgtgacccccccaggagaagctgggaa accaagcctatagtcaggccgagaacgccatggcacggaagaagccatgctgcctgtgag cccctcagaggacactgagtcaaaaaaccccacgcgcttggaggcgcaggatgggaaaag aaggtggcgaccttccccacccttcaatctggggcctgaactggagat ->ZKC2/2016 +>KX253996 agttgttgatctgtgtgaatcagactgcgacagttcgagtttgaagcgaaagctagcaac agtatcaacaggttttattttggatttggaaacgagagtttctggtcatgaaaaacccaa aaaagaaatccggaggattccggattgtcaatatgctaaaacgcggagtagcccgtgtga @@ -1076,7 +1076,7 @@ ggcctgaactggagatcagctgtggatctccagaagagggactagtggttagaggagacc ccccggaaaacgcaaaacagcatattgacgctgggaaagaccagagactccatgagtttc caccacgctggccgccaggcacagatcgccgaatagcggcggccggtgtggggaaatcca tgggtct ->VEN/UF_1/2016 +>KX702400 agttgttactgttgctgactcagactgcgacagttcgagtttgaagcgaaagctagcaac agtatcaacaggttttattttggatttggaaacgagagtttctggtcatgaaaaacccaa aaaagaaatccggaggattccggattgtcaatatgctaaaacgcggagtagcccgtgtga @@ -1258,7 +1258,7 @@ ggcctgaactggagatcagctgtggatctccagaagagggactagtggttagaggagacc ccccggaaaacgcaaaacagcatattgacgctgggaaagaccagagactccatgagtttc caccacgctggccgccaggcacagatcgccgaatagcggcggccggtgtggggaaatcca tgggtctt ->DOM/2016/BB_0059 +>KY785425 tggctgccatgctgagaataatcaatgctaggaaggagaagaagagacgaggcgcagata ctagtgtcggaattgttggcctcctgctgaccacagctatggcagcggaggtcactagac gtgggagtgcatactacatgtacttggacagaaacgatgctggggaggccatatctttcc @@ -1427,7 +1427,7 @@ ggtgtggatctctcatagggcacagaccgcgcaccacctgggctgagaacattaaaaaca cagtcaacatggtgcgcaggatcataggtgaggaagaaaagtacatggactacctatcca cccaagttcgctacttgggtgaagaagggtctacacctggagtgctgtaagcaccaatct taatgttgtcaggcc ->BRA/2016/FC_6706 +>KY785433 agtttgaagcgaaagctagcaacagtatcaacaggttttatttyggatttggaaacgaga gtttctggtcatgaaaaacccaaaaaagaaatccggaggattccggattgtcaatatgct aaaacgcggagtagcccgtgtgagcccctttgggggcttgaagaggctgccagccggact @@ -1601,7 +1601,7 @@ cattccctatttgggaaaaagggaagacttgtggtgtggatctctcatagggcacagacc gcgcaccacctgggctgagaacattaaaaacacagtcaacatggtgcgcaggatcatagg tgatgaagaaaagtacatggactacctatccacccaagttcgctacttgggtgaagaagg gtctacacctggagtgctgtaagcaccaatcttaatgttgtcaggc ->DOM/2016/BB_0183 +>KY785420 gtttgaagcgaaagctagcaacagtatcaacaggttttattttggatttggaaacgagag tttctggtcatgaaaaacccaaaaaagaaatccggaggattccggattgtcaatatgcta aaacgcggagtagcccgtgtgagcccctttgggggcttgaagaggctgccagccggactt @@ -1780,7 +1780,7 @@ tagtcaggccgagaacgccatggcacggaagaagccatgctgcctgtgagcccctcagag gacactgagtcaaaaaaccccacgcgcttggaggcgcaggatgggaaaagaaggtggcga ccttccccacccttcaatctggggcctgaactggagatcagctgtggatccccagaagag g ->EcEs062_16 +>KX879603 agtagttgatctgtgtgaatcagactgcgacagttcgagtttgaagcgaaagctagcaac agtatcaacaggttttattttggatttggaaacgagagtttctggtcatgaaaaacccaa aaaagaaatccggaggattccggattgtcaatatgctaaaacgcggagtagcccgtgtga @@ -1962,7 +1962,7 @@ ggcctgaactggagatcagctgtggatctccagaagagggactagtggttagaggagacc ccccggaaaacgcaaaacagcatattgacgctgggaaagaccagagactccatgagtttc caccacgctggccgccaggcacagatcgccgaatagcggcggccggtgtggggaaatcca tgggagatcgga ->HND/2016/HU_ME59 +>KY785418 gtttgaagcgaaagctagcaacagtatcaacaggttttattttggatttggaaacgagag tttctggtcatgaaaaacccaaaaaagaaatccggaggattccggattgtcaatatgcta aaacgcggagtagcccgtgtgagcccctttgggggcttgaagaggctgccagccggactt @@ -2136,7 +2136,7 @@ attccctatttgggaaaaagggaagacttgtggtgtggatctctcatagggcacagaccg cgcaccacctgggctgagaacattaaaaacacagtcaacatggtgcgcaggatcataggt gatgaagaaaagtacatggactacctatccacccaagttcgctacttgggtgaagaaggg tctacacctggagtgctgtaagcaccaatcttaatgttgtcaggc ->DOM/2016/MA_WGS16_011 +>KY785484 aagcgaaagctagcaacagtatcaacaggttttattttggatttggaaacgagagtttct ggtcatgaaaaacccaaaaaagaaatccggaggattccggattgtcaatatgctaaaacg cggagtagcccgtgtgagcccctttgggggcttgaagaggctgccagccggacttctgct @@ -2314,7 +2314,7 @@ ggggaaagctgtgcagcctgtgacccccccaggagaagctgggaaaccaagcctatagtc aggccgagaacgccatggcacggaagaagccatgctgcctgtgagcccctcagaggacac tgagtcaaaaaaccccacgcgcttggaggcgcaggatgggaaaagaaggtggcgaccttc cccacccttcaatctggggcctgaactggggatcag ->DOM/2016/BB_0433 +>KY785441 tttgaagcgaaagctagcaacagtatcaacaggttttattttggatttggaaacgagagt ttctggtcatgaaaaacccaaaaaagaaatccggaggattccggattgtcaatatgctaa aacgcggagtagcccgtgtgagcccctttgggggcttgaagaggctgccagccggacttc @@ -2488,7 +2488,7 @@ ttccctatttgggaaaaagggaagacttgtggtgtggatctctcatagggcacagaccgc gcaccacctgggctgagaacattaaaaacacagtcaacatggtgcgcaggatcataggtg aggaagaaaagtacatggactacctatccacccaagttcgctacttgggtgaagaagggt ctacacctggagtgctgtaagcaccaatcctaatgttgtcaggcc ->USA/2016/FL022 +>KY075935 gcgacagttcgagtttgaagcgaaagctagcaacagtatcaacaggttttattttggatt tggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggaggattccggatt gtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaagaggctg @@ -2662,7 +2662,7 @@ aaatggacagacattccctatttgggaaaaagggaagacttgtggtgtggatctctcata gggcacagaccgcgcaccacctgggctgagaacattaaaaacacagtcaacatggtgcgc aggatcataggtgaggaagaaaagtacatggactacctatccacccaagtccgctacttg ggtgaagaagggtctacacctggagtgctgtaagcaccaatctta ->SG_027 +>KY241697 ctgcgacagttcgagtttgaagcgaaagctagcaacagtatcaacaggttttattttgga tttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggaggattccgga ttgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaagaggc @@ -2842,7 +2842,7 @@ tgagcccctcagaggacactgagtcaaaaaaccccacgcgcttggaggcgcaggatggga aaagaaggtggcgaccttccccacccttcaatctggggcctgaactggagatcagctgtg gatctccagaagagggactagtggttagaggagaccccccggaaaacgcaaaacagcata ttgacgctgggaaagaccagagactccatgagtttccaccacgctggccgccag ->SG_074 +>KY241744 gaatcagactgcgacagttcgagtttgaagcgaaagctagcaacagtatcaacaggtttt attttggatttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggagg attccggattgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggggctt @@ -3023,7 +3023,7 @@ ggatgggaaaagaaggtggcgaccttccccacccttcaatctggggcctgaactggagat cagctgtggatctccagaagagggactagtggttagaggagaccccccggaaaacgcaaa acagcatattgacgctgggaaagaccagagactccatgagtttccaccacgctggccgcc aggcacagatcgccgaatagcg ->SG_056 +>KY241726 gaatcagactgcgacagttcgagtttgaagcgaaagctagcaacagtatcaacaggtttt attttggatttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggagg attccggattgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggggctt @@ -3203,7 +3203,7 @@ gctgcctgtgagcccctcagaggacactgagtcaaaaaaccccacgcgcttggaggcgca ggatgggaaaagaaggtggcgaccttccccacccttcaatctggggcctgaactggagat cagctgtggatctccagaagagggactagtggttagaggagaccccccggaaaacgcaaa acagcatattgacgctgggaaagaccagagactccatgagtttccaccacgctggcc ->USA/2016/FLUR022 +>KY325473 gtgtgaatcagactgcgacagttcgagtttgaagcgaaagctagcaacagtatcaacagg ttttattttggatttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccg gaggattccggattgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggg @@ -3384,7 +3384,7 @@ cgcaggatgggaaaagaaggtggcgaccttccccacccttcaatctggggcctgaactgg agatcagctgtggatctccagaagagggactagtggttagaggagaccccccggaaaacg caaaacagcatattgacgctgggaaagaccagagactccatgagtttccaccacgctggc cgccaggcacagatcgccgaatagcggcggccggtgtggggaaatc ->Aedes_aegypti/USA/2016/FL05 +>KY075937 gacagttcgagtttgaagcgaaagctagcaacagtatcaacaggttttattttggatttg gaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggaggattccggattgt caatatgctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaagaggctgcc @@ -3562,7 +3562,7 @@ agtcagccacagcttggggaaagctgtgcagcctgtgacccccccaggagaagctgggaa accaagcctatagtcaggccgagaacgccatggcacggaagaagccatgctgcctgtgag cccctcagaggacactgagtcaaaaaaccccacgcgcttggaggcgcaggatgggaaaag aaggtggcgaccttccccacccttcaatctggggcctgaactggagat ->SG_018 +>KY241688 atgnnnnnnnnnnnnnnnnnnnccggaggattccggattgtcaatatgctaaaacgcgga gtagcccgtgtgagcccctttgggggcttgaagaggctgccagccggacttctgctgggt catgggcccatcaggatggtcttggcgattctagcctttttgaggttcacggcaatcaag @@ -3741,7 +3741,7 @@ tcaaaaaaccccacgcgcttggaggcgcaggatgggaaaagaaggtggcgaccttcccca cccttcaatctggggcctgaactggagatcagctgtggatctccagaagagggactagtg gttagaggagaccccccggaaaacgcaaaacagcatattgacgctgggaaagaccagaga ctccatgagtttccaccacgctggccgccaggcacagat ->USA/2016/FLWB042 +>KY325478 ctttgggggcttgaagaggctgccagccggacttctgctgggtcatgggcccatcaggat ggtcttggcgattctagcctttttgagattcacggcaatcaagccatcactgggtctcat caatagatggggttcagtggggaaaaaagaggctatggaaataataaagaagttcaagaa @@ -3916,7 +3916,7 @@ aatctcaatgttgtcaggcctgctagtcagccacagcttggggaaagctgtgcagcctgt gacccccccaggagaagctgggaaaccaagcctatagtcaggccgagaacgccatggcac ggaagaagccatgctgcctgtgagcccctcagaggacactgagtcaaaaaaccccacgcg cttggaggcgcaggnnnnnnaaagaag ->COL/PRV_00028/2015 +>MF574578 ttgaagcgaaagctagcaacagtatcaacaggttttattttggatttggaaacgagagtt tctggtcatgaaaaacccaaaaaagaaatccggaggattccggattgtcaatatgctaaa acgcggagtagcccgtgtgagcccctttgggggcttgaagaggctgccagccggacttct @@ -4095,7 +4095,7 @@ gtcaggccgagaacgccatggcacggaagaagccatgctgcctgtgagcccctcagagga cactgagtcaaaaaaccccacgcgcttggaggcgcaggatgggaaaagaaggtggcgacc ttccccacccttcaatctggggcctgaactggagatcagctgtggatctccagaagaggg actagtggttagaggaga ->Thailand/1610acTw +>MF692778 gcaacagtatcaacaggttttattttggatttggaaacgagagtttctggtcatgaaaaa cccaaaaaagaaatccggaggattccggattgtcaatatgctaaaacgcggagtagcccg tgtgagcccctttgggggcttgaagaggctgccagccggacttctgctgggccatgggcc @@ -4271,7 +4271,7 @@ ggactacctatccacccaagttcgctacttgggtgaagaagggtctacacctggagtgct gtaagcaccaatcttagtgttgtcaggcctgctagtcagccacagcttggggaaagctgt gcagcctgtgacccccccaggagaagctgggaaaccaagcccatagtcaggccgagaacg ccatggcacggaag ->1_0087_PF +>KX447509 agtatcaacaggttttattttggatttggaaacgagagtttctggtcatgaaaaacccaa aaaagaaatccggaggattccggattgtcaatatgctaaaacgcggagtagcccgtgtga gcccctttgggggcttgaagaggctgccagccggacttctgctgggtcatgggcccatca @@ -4449,7 +4449,7 @@ ctgtgacccccccaggagaagctgggaaaccaagcctatagtcaggccgagaacgccatg gcacggaagaagccatgctgcctgtgagcccctcagaggacactgagtcaaaaaacccca cgcgcttggaggcgcaggatgggaaaagaaggtggcgaccttccccacccttcaatctgg ggcctgaactggagatcagctgtggat ->1_0199_PF +>KX447519 actgcgacagttcgagtttgaagcgaaagctagcaacagtatcaacaggttttattttgg atttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggaggattccgg attgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaagagg @@ -4603,7 +4603,7 @@ tgggctctagtggacaaggaaagagagcaccacctgagaggagagtgccagagttgtgtg tacaacatgatgggaaaaagagaaaagaaacaaggggaatttggaaaggccaagggcagc cgcgccatctggtatatgtggctaggggctagatttctagagttcgaagcccttggattc ttgaacgaggatcactggatgg ->1_0181_PF +>KX447512 agtatcaacaggttttattttggatttggaaacgagagtttctggtcatgaaaaacccaa aaaagaaatccggaggattccggattgtcaatatgctaaaacgcggagtagcccgtgtga gcccctttgggggcttgaagaggctgccagccggacttctgctgggtcatgggcccatca @@ -4781,7 +4781,7 @@ ctgtgacccccccaggagaagctgggaaaccaagcctatagtcaggccgagaacgccatg gcacggaagaagccatgctgcctgtgagcccctcagaggacactgagtcaaaaaacccca cgcgcttggaggcgcaggatgggaaaagaaggtggcgaccttccccacccttcaatctgg ggcctgaactggagatcagctgtgga ->Brazil/2015/ZBRC301 +>KY558995 gatttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggaggattccg gattgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaagag gctgccagccggacttctgctgggtcatgggcccatcaggatggtcttggcgattctagc @@ -4950,7 +4950,7 @@ gactgcttgcctagcaaaatcatatgcgcagatgtggcagctcctttatttccacagaan ggacctccgactgatggccaatgccatttgttcatctgtgccagttgactgggttccaac tgggagaactacctggtcaatccatggaaanggagaatggatgaccactgaagacatgct tg ->Brazil/2015/ZBRA105 +>KY558989 gatttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggaggattccg gattgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaagag gctgccagccggacttctgctgggtcatgggcccatcaggatggtcttggcgattctagc @@ -5119,7 +5119,7 @@ gactgcttgcctagcaaaatcatatgcgcaaatgtggcagctcctttatttccacagaag ggacctccgactgatggccaatgccatttgttcatctgtgccagttgactgggttccaac tgggagaactacctggtcaatccatggaaagggagaatggatgaccactgaagacatgct tg ->Brazil/2016/ZBRC16 +>KY558991 tgagaataatcaatgctaggaaggagaagaagagacgaggcgcagatactagtgtcggaa ttgttggcctcctgctgaccacagctatggcagcggaggtcactagacgtgggagtgcat actatatgtacttggacagaaacgatgctggggaggccatatcttttccaaccacattgg @@ -5272,7 +5272,7 @@ atgcagatgacactgctggctgggacacccgcatcagcaggtttgatctggagaatgaag ctctaatcaccaaccaaatggagagagggcacagggccttggcattggccataatcaagt acacataccaaaacaaagtggtaaaggtccttagaccagctgaaaaagggaaaacagtta tggacatcatttcgagacaagaccaaaggggg ->V8375 +>KU501217 atgaaaaacccaaaaaagaaatccggaggattccggattgtcaatatgctaaaacgcgga gtagcccgtgtgagcccctttgggggcttgaagaggctgccagccggacttctgctgggt catgggcccatcaggatggtcttggcgattctagcctttttgagattcacggcaatcaag @@ -5445,7 +5445,7 @@ ttgggaaaaagggaagacttgtggtgtggatctctcatagggcacagaccgcgcaccacc tgggctgagaacattaaaaacacagtcaacatggtgcgcaggatcataggtgatgaagaa aagtacatggactacctatccacccaagttcgctacttgggtgaagaagggtctacacct ggagtgctgtaa ->Nica1_16 +>KX421195 tcgagtttgaagcgaaagctagcaacagtatcaacaggttttattttggatttggaaacg agagtttctggtcatgaaaaacccaaaaaagaaatccggaggattccggattgtcaatat gctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaagaggctgccagccgg @@ -5624,7 +5624,7 @@ cctatagtcaggccgagaacgccatggcacggaagaagccatgctgcctgtgagcccctc agaggacactgagtcaaaaaaccccacgcgcttggaggcgcaggatgggaaaagaaggtg gcgaccttccccacccttcaatctggggcctgaactggagatcagctgtggatctccaga agagggactagtggttagaggag ->Brazil/2015/ZBRC303 +>KY558997 tgagaataatcaatgctaggaaggagaagaagagacgaggcacagatactagtgtcggaa ttgttggcctcctgctgaccacagctatggcagcggaggtcactagacgtgggagtgcat actatatgtacttggacagaaacgatgctggggaggccatatcttttccaaccacattgg @@ -5782,7 +5782,7 @@ agatgcaagacttgtggctgctgcggaggtcagagaaagtgaccaactggttgcagagca acggatgggataggctcaaacgaatggcagtcagtggagatgattgcgttgtgaagccaa ttgatgataggtttgcacatgccctcaggttcttgaatgatatgggaaaagttaggaagg acacacaagagtgg ->SMGC_1 +>KX266255 tctgtgtgaatcagactgcgacagttcgagtttgaagcgaaagctagcaacagtatcaac aggttttattttggatttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaat ccggaggattccggattgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttg