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Incorporated some changes suggested by comment: #203 (comment) * Fixed pathogen.json for genotype-level dataset to include the example sequences fasta nextstrain/dengue@c029f1d * Enabled stop and frameshift QC nextstrain/dengue@90523a7 * Include reconstructed ancestor for the genotype-level dataset nextstrain/dengue@616979c
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##gff-version 3 | ||
##sequence-region NC_001477.1 1 10735 | ||
NC_001477.1 feature gene 95 436 . + . codon_start=1;gene=C;gene_name=C; | ||
NC_001477.1 feature gene 437 709 . + . codon_start=1;gene=pr;gene_name=pr; | ||
NC_001477.1 feature gene 437 934 . + . codon_start=1;gene=M;gene_name=M; | ||
NC_001477.1 feature gene 935 2419 . + . codon_start=1;gene=E;gene_name=E; | ||
NC_001477.1 feature gene 2420 3475 . + . codon_start=1;gene=NS1;gene_name=NS1; | ||
NC_001477.1 feature gene 3476 4129 . + . codon_start=1;gene=NS2A;gene_name=NS2A; | ||
NC_001477.1 feature gene 4130 4519 . + . codon_start=1;gene=NS2B;gene_name=NS2B; | ||
NC_001477.1 feature gene 4520 6376 . + . codon_start=1;gene=NS3;gene_name=NS3; | ||
NC_001477.1 feature gene 6377 6757 . + . codon_start=1;gene=NS4A;gene_name=NS4A; | ||
NC_001477.1 feature gene 6758 6826 . + . codon_start=1;gene=2K;gene_name=2K; | ||
NC_001477.1 feature gene 6827 7573 . + . codon_start=1;gene=NS4B;gene_name=NS4B; | ||
NC_001477.1 feature gene 7574 10270 . + . codon_start=1;gene=NS5;gene_name=NS5; | ||
##sequence-region Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome 1 10649 | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 102 440 . + . codon_start=1;gene=C;gene_name=C; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 441 713 . + . codon_start=1;gene=pr;gene_name=pr; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 441 938 . + . codon_start=1;gene=M;gene_name=M; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 939 2423 . + . codon_start=1;gene=E;gene_name=E; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 2424 3479 . + . codon_start=1;gene=NS1;gene_name=NS1; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 3480 4133 . + . codon_start=1;gene=NS2A;gene_name=NS2A; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 4134 4523 . + . codon_start=1;gene=NS2B;gene_name=NS2B; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 4524 6377 . + . codon_start=1;gene=NS3;gene_name=NS3; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 6378 6758 . + . codon_start=1;gene=NS4A;gene_name=NS4A; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 6759 6827 . + . codon_start=1;gene=2K;gene_name=2K; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 6828 7562 . + . codon_start=1;gene=NS4B;gene_name=NS4B; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 7563 10262 . + . codon_start=1;gene=NS5;gene_name=NS5; |
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##gff-version 3 | ||
##sequence-region NC_001474.2 1 10723 | ||
NC_001474.2 feature gene 97 438 . + . codon_start=1;gene=C;gene_name=C; | ||
NC_001474.2 feature gene 439 711 . + . codon_start=1;gene=pr;gene_name=pr; | ||
NC_001474.2 feature gene 439 936 . + . codon_start=1;gene=M;gene_name=M; | ||
NC_001474.2 feature gene 937 2421 . + . codon_start=1;gene=E;gene_name=E; | ||
NC_001474.2 feature gene 2422 3477 . + . codon_start=1;gene=NS1;gene_name=NS1; | ||
NC_001474.2 feature gene 3478 4131 . + . codon_start=1;gene=NS2A;gene_name=NS2A; | ||
NC_001474.2 feature gene 4132 4521 . + . codon_start=1;gene=NS2B;gene_name=NS2B; | ||
NC_001474.2 feature gene 4522 6375 . + . codon_start=1;gene=NS3;gene_name=NS3; | ||
NC_001474.2 feature gene 6376 6756 . + . codon_start=1;gene=NS4A;gene_name=NS4A; | ||
NC_001474.2 feature gene 6757 6825 . + . codon_start=1;gene=2K;gene_name=2K; | ||
NC_001474.2 feature gene 6826 7569 . + . codon_start=1;gene=NS4B;gene_name=NS4B; | ||
NC_001474.2 feature gene 7570 10269 . + . codon_start=1;gene=NS5;gene_name=NS5; | ||
##sequence-region Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome 1 10649 | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 102 440 . + . codon_start=1;gene=C;gene_name=C; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 441 713 . + . codon_start=1;gene=pr;gene_name=pr; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 441 938 . + . codon_start=1;gene=M;gene_name=M; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 939 2423 . + . codon_start=1;gene=E;gene_name=E; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 2424 3479 . + . codon_start=1;gene=NS1;gene_name=NS1; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 3480 4133 . + . codon_start=1;gene=NS2A;gene_name=NS2A; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 4134 4523 . + . codon_start=1;gene=NS2B;gene_name=NS2B; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 4524 6377 . + . codon_start=1;gene=NS3;gene_name=NS3; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 6378 6758 . + . codon_start=1;gene=NS4A;gene_name=NS4A; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 6759 6827 . + . codon_start=1;gene=2K;gene_name=2K; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 6828 7562 . + . codon_start=1;gene=NS4B;gene_name=NS4B; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 7563 10262 . + . codon_start=1;gene=NS5;gene_name=NS5; |
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##gff-version 3 | ||
##sequence-region NC_001475.2 1 10707 | ||
NC_001475.2 feature gene 95 436 . + . codon_start=1;gene=C;gene_name=C; | ||
NC_001475.2 feature gene 437 709 . + . codon_start=1;gene=pr;gene_name=pr; | ||
NC_001475.2 feature gene 437 934 . + . codon_start=1;gene=M;gene_name=M; | ||
NC_001475.2 feature gene 935 2419 . + . codon_start=1;gene=E;gene_name=E; | ||
NC_001475.2 feature gene 2414 3469 . + . codon_start=1;gene=NS1;gene_name=NS1; | ||
NC_001475.2 feature gene 3470 4123 . + . codon_start=1;gene=NS2A;gene_name=NS2A; | ||
NC_001475.2 feature gene 4124 4513 . + . codon_start=1;gene=NS2B;gene_name=NS2B; | ||
NC_001475.2 feature gene 4514 6370 . + . codon_start=1;gene=NS3;gene_name=NS3; | ||
NC_001475.2 feature gene 6371 6751 . + . codon_start=1;gene=NS4A;gene_name=NS4A; | ||
NC_001475.2 feature gene 6752 6820 . + . codon_start=1;gene=2K;gene_name=2K; | ||
NC_001475.2 feature gene 6821 7564 . + . codon_start=1;gene=NS4B;gene_name=NS4B; | ||
NC_001475.2 feature gene 7565 10264 . + . codon_start=1;gene=NS5;gene_name=NS5; | ||
##sequence-region Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome 1 10649 | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 102 440 . + . codon_start=1;gene=C;gene_name=C; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 441 713 . + . codon_start=1;gene=pr;gene_name=pr; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 441 938 . + . codon_start=1;gene=M;gene_name=M; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 939 2423 . + . codon_start=1;gene=E;gene_name=E; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 2424 3479 . + . codon_start=1;gene=NS1;gene_name=NS1; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 3480 4133 . + . codon_start=1;gene=NS2A;gene_name=NS2A; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 4134 4523 . + . codon_start=1;gene=NS2B;gene_name=NS2B; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 4524 6377 . + . codon_start=1;gene=NS3;gene_name=NS3; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 6378 6758 . + . codon_start=1;gene=NS4A;gene_name=NS4A; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 6759 6827 . + . codon_start=1;gene=2K;gene_name=2K; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 6828 7562 . + . codon_start=1;gene=NS4B;gene_name=NS4B; | ||
Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome feature gene 7563 10262 . + . codon_start=1;gene=NS5;gene_name=NS5; |
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