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flu: fix clade 2a.3b and add glyc to old data sets
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rneher committed Feb 1, 2023
1 parent e69cefe commit b55e22a
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##gff-version 3
##sequence-region CY121680.1 1 1752
CY121680.1 feature gene 21 71 . + . gene_name="SigPep"
CY121680.1 feature gene 72 1052 . + . gene_name="HA1"
CY121680.1 feature gene 1053 1718 . + . gene_name="HA2"
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Country (Institute),Target,Oligonucleotide,Sequence
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{
"schemaVersion": "1.2.0",
"privateMutations": {
"enabled": true,
"typical": 5,
"cutoff": 15,
"weightLabeledSubstitutions": 2,
"weightReversionSubstitutions": 1,
"weightUnlabeledSubstitutions": 1
},
"missingData": {
"enabled": false,
"missingDataThreshold": 100,
"scoreBias": 10
},
"snpClusters": {
"enabled": false,
"windowSize": 100,
"clusterCutOff": 5,
"scoreWeight": 50
},
"mixedSites": {
"enabled": true,
"mixedSitesThreshold": 4
},
"frameShifts": {
"enabled": true
},
"stopCodons": {
"enabled": true,
"ignoredStopCodons": []
}
}
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>CY121680.1 Influenza A virus (A/California/07/2009(H1N1)) hemagglutinin (HA) gene, complete cds
GGAAAACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACACCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGTCATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCGAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAAACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATATCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGCTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAACATTAGGATTTCAGAAGCATGAGAAAAACAC

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{
"tag": "2023-02-01T12:00:00Z",
"comment": "New WHO clade names, data from GISAID",
"compatibility": {
"nextcladeCli": {
"min": "1.3.0",
"max": null
},
"nextcladeWeb": {
"min": "1.6.0",
"max": null
}
},
"enabled": true,
"files": {
"geneMap": "genemap.gff",
"primers": "primers.csv",
"qc": "qc.json",
"reference": "reference.fasta",
"sequences": "sequences.fasta",
"tree": "tree.json",
"virusPropertiesJson": "virus_properties.json"
},
"metadata": {}
}
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