diff --git a/genomics/4-Variation/selection_analysis_ncbi.bed b/genomics/4-Variation/selection_analysis_ncbi.bed new file mode 100644 index 00000000..ea51baf1 --- /dev/null +++ b/genomics/4-Variation/selection_analysis_ncbi.bed @@ -0,0 +1,307 @@ +NC_045512.2 21583 21585 Positive_selection 1 +NC_045512.2 21646 21648 Positive_selection 1 +NC_045512.2 21709 21711 Positive_selection 2 +NC_045512.2 21709 21711 Intra-host_variants 2 +NC_045512.2 21787 21789 Positive_selection 1 +NC_045512.2 21829 21831 Positive_selection 1 +NC_045512.2 21844 21846 Positive_selection 1 +NC_045512.2 21988 21990 Positive_selection 2 +NC_045512.2 21988 21990 Unexpected_residues 2 +NC_045512.2 21994 21996 Positive_selection 2 +NC_045512.2 21994 21996 Intra-host_variants 2 +NC_045512.2 22660 22662 Positive_selection 3 +NC_045512.2 22660 22662 Multiple_Clades 3 +NC_045512.2 22660 22662 Intra-host_variants 3 +NC_045512.2 22876 22878 Positive_selection 1 +NC_045512.2 23401 23403 Common_Variant 2 +NC_045512.2 23401 23403 Increasing_frequency 2 +NC_045512.2 23404 23406 Positive_selection 2 +NC_045512.2 23404 23406 Unexpected_residues 2 +NC_045512.2 23677 23679 Positive_selection 1 +NC_045512.2 24052 24054 Positive_selection 2 +NC_045512.2 24052 24054 Increasing_frequency 2 +NC_045512.2 24094 24096 Positive_selection 2 +NC_045512.2 24094 24096 Intra-host_variants 2 +NC_045512.2 24388 24390 Positive_selection 2 +NC_045512.2 24388 24390 Multiple_Clades 2 +NC_045512.2 24679 24681 Positive_selection 2 +NC_045512.2 24679 24681 Unexpected_residues 2 +NC_045512.2 24931 24933 Positive_selection 3 +NC_045512.2 24931 24933 Multiple_Clades 3 +NC_045512.2 24931 24933 Unexpected_residues 3 +NC_045512.2 28309 28311 Positive_selection 4 +NC_045512.2 28309 28311 Multiple_Clades 4 +NC_045512.2 28309 28311 Increasing_frequency 4 +NC_045512.2 28309 28311 Intra-host_variants 4 +NC_045512.2 28330 28332 Positive_selection 1 +NC_045512.2 28336 28338 Positive_selection 2 +NC_045512.2 28336 28338 Increasing_frequency 2 +NC_045512.2 28372 28374 Positive_selection 3 +NC_045512.2 28372 28374 Multiple_Clades 3 +NC_045512.2 28372 28374 Unexpected_residues 3 +NC_045512.2 28594 28596 Negative_selection 1 +NC_045512.2 28627 28629 Positive_selection 2 +NC_045512.2 28627 28629 Intra-host_variants 2 +NC_045512.2 28702 28704 Positive_selection 1 +NC_045512.2 28723 28725 Positive_selection 3 +NC_045512.2 28723 28725 Unexpected_residues 3 +NC_045512.2 28723 28725 Intra-host_variants 3 +NC_045512.2 28810 28812 Positive_selection 1 +NC_045512.2 28825 28827 Positive_selection 2 +NC_045512.2 28825 28827 Unexpected_residues 2 +NC_045512.2 28840 28842 Positive_selection 1 +NC_045512.2 28849 28851 Positive_selection 3 +NC_045512.2 28849 28851 Increasing_frequency 3 +NC_045512.2 28849 28851 Intra-host_variants 3 +NC_045512.2 28861 28863 Positive_selection 4 +NC_045512.2 28861 28863 Multiple_Clades 4 +NC_045512.2 28861 28863 Increasing_frequency 4 +NC_045512.2 28861 28863 Intra-host_variants 4 +NC_045512.2 28876 28878 Positive_selection 3 +NC_045512.2 28876 28878 Unexpected_residues 3 +NC_045512.2 28876 28878 Intra-host_variants 3 +NC_045512.2 28885 28887 Positive_selection 2 +NC_045512.2 28885 28887 Increasing_frequency 2 +NC_045512.2 28894 28896 Positive_selection 2 +NC_045512.2 28894 28896 Increasing_frequency 2 +NC_045512.2 28924 28926 Positive_selection 1 +NC_045512.2 29302 29304 Positive_selection 2 +NC_045512.2 29302 29304 Multiple_Clades 2 +NC_045512.2 29413 29415 Positive_selection 1 +NC_045512.2 29449 29451 Positive_selection 2 +NC_045512.2 29449 29451 Intra-host_variants 2 +NC_045512.2 29476 29478 Positive_selection 1 +NC_045512.2 26780 26782 Positive_selection 1 +NC_045512.2 27044 27046 Positive_selection 2 +NC_045512.2 27044 27046 Increasing_frequency 2 +NC_045512.2 27146 27148 Positive_selection 1 +NC_045512.2 25428 25430 Positive_selection 2 +NC_045512.2 25428 25430 Increasing_frequency 2 +NC_045512.2 25431 25433 Positive_selection 3 +NC_045512.2 25431 25433 Increasing_frequency 3 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Unexpected_residues 3 +NC_045512.2 25710 25712 Intra-host_variants 3 +NC_045512.2 25719 25721 Positive_selection 2 +NC_045512.2 25719 25721 Unexpected_residues 2 +NC_045512.2 25764 25766 Negative_selection 1 +NC_045512.2 25782 25784 Negative_selection 1 +NC_045512.2 25809 25811 Positive_selection 2 +NC_045512.2 25809 25811 Unexpected_residues 2 +NC_045512.2 25821 25823 Positive_selection 2 +NC_045512.2 25821 25823 Unexpected_residues 2 +NC_045512.2 25830 25832 Positive_selection 2 +NC_045512.2 25830 25832 Unexpected_residues 2 +NC_045512.2 25884 25886 Positive_selection 1 +NC_045512.2 25941 25943 Positive_selection 1 +NC_045512.2 25944 25946 Positive_selection 2 +NC_045512.2 25944 25946 Unexpected_residues 2 +NC_045512.2 26028 26030 Positive_selection 1 +NC_045512.2 26043 26045 Positive_selection 1 +NC_045512.2 26106 26108 Positive_selection 1 +NC_045512.2 26142 26144 Positive_selection 3 +NC_045512.2 26142 26144 Multiple_Clades 3 +NC_045512.2 26142 26144 Unexpected_residues 3 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955 957 Positive_selection 2 +NC_045512.2 955 957 Unexpected_residues 2 +NC_045512.2 1057 1059 Positive_selection 4 +NC_045512.2 1057 1059 Multiple_Clades 4 +NC_045512.2 1057 1059 Increasing_frequency 4 +NC_045512.2 1057 1059 Intra-host_variants 4 +NC_045512.2 1066 1068 Positive_selection 1 +NC_045512.2 1120 1122 Negative_selection 1 +NC_045512.2 1384 1386 Positive_selection 2 +NC_045512.2 1384 1386 Unexpected_residues 2 +NC_045512.2 1438 1440 Positive_selection 2 +NC_045512.2 1438 1440 Increasing_frequency 2 +NC_045512.2 1546 1548 Positive_selection 1 +NC_045512.2 1567 1569 Negative_selection 1 +NC_045512.2 1603 1605 Negative_selection 1 +NC_045512.2 1819 1821 Positive_selection 2 +NC_045512.2 1819 1821 Multiple_Clades 2 +NC_045512.2 2002 2004 Positive_selection 3 +NC_045512.2 2002 2004 Unexpected_residues 3 +NC_045512.2 2002 2004 Intra-host_variants 3 +NC_045512.2 2242 2244 Positive_selection 3 +NC_045512.2 2242 2244 Unexpected_residues 3 +NC_045512.2 2242 2244 Intra-host_variants 3 +NC_045512.2 3034 3036 Negative_selection 3 +NC_045512.2 3034 3036 Common_Variant 3 +NC_045512.2 3034 3036 Intra-host_variants 3 +NC_045512.2 3142 3144 Positive_selection 1 +NC_045512.2 3370 3372 Positive_selection 3 +NC_045512.2 3370 3372 Increasing_frequency 3 +NC_045512.2 3370 3372 Intra-host_variants 3 +NC_045512.2 3562 3564 Positive_selection 4 +NC_045512.2 3562 3564 Multiple_Clades 4 +NC_045512.2 3562 3564 Increasing_frequency 4 +NC_045512.2 3562 3564 Unexpected_residues 4 +NC_045512.2 4009 4011 Positive_selection 2 +NC_045512.2 4009 4011 Unexpected_residues 2 +NC_045512.2 4252 4254 Negative_selection 1 +NC_045512.2 4387 4389 Positive_selection 1 +NC_045512.2 5059 5061 Positive_selection 1 +NC_045512.2 5605 5607 Negative_selection 1 +NC_045512.2 6253 6255 Positive_selection 2 +NC_045512.2 6253 6255 Multiple_Clades 2 +NC_045512.2 6310 6312 Positive_selection 3 +NC_045512.2 6310 6312 Multiple_Clades 3 +NC_045512.2 6310 6312 Increasing_frequency 3 +NC_045512.2 6634 6636 Positive_selection 3 +NC_045512.2 6634 6636 Multiple_Clades 3 +NC_045512.2 6634 6636 Intra-host_variants 3 +NC_045512.2 6694 6696 Positive_selection 2 +NC_045512.2 6694 6696 Multiple_Clades 2 +NC_045512.2 6721 6723 Positive_selection 3 +NC_045512.2 6721 6723 Multiple_Clades 3 +NC_045512.2 6721 6723 Increasing_frequency 3 +NC_045512.2 6988 6990 Positive_selection 3 +NC_045512.2 6988 6990 Multiple_Clades 3 +NC_045512.2 6988 6990 Increasing_frequency 3 +NC_045512.2 7009 7011 Positive_selection 3 +NC_045512.2 7009 7011 Multiple_Clades 3 +NC_045512.2 7009 7011 Increasing_frequency 3 +NC_045512.2 7987 7989 Negative_selection 1 +NC_045512.2 8779 8781 Negative_selection 2 +NC_045512.2 8779 8781 Intra-host_variants 2 +NC_045512.2 8788 8790 Positive_selection 2 +NC_045512.2 8788 8790 Multiple_Clades 2 +NC_045512.2 9109 9111 Positive_selection 1 +NC_045512.2 9436 9438 Positive_selection 3 +NC_045512.2 9436 9438 Multiple_Clades 3 +NC_045512.2 9436 9438 Intra-host_variants 3 +NC_045512.2 10321 10323 Positive_selection 4 +NC_045512.2 10321 10323 Multiple_Clades 4 +NC_045512.2 10321 10323 Increasing_frequency 4 +NC_045512.2 10321 10323 Intra-host_variants 4 +NC_045512.2 10333 10335 Positive_selection 1 +NC_045512.2 10711 10713 Positive_selection 1 +NC_045512.2 11071 11073 Negative_selection 2 +NC_045512.2 11071 11073 Intra-host_variants 2 +NC_045512.2 11080 11082 Positive_selection 2 +NC_045512.2 11080 11082 Intra-host_variants 2 +NC_045512.2 11404 11406 Positive_selection 2 +NC_045512.2 11404 11406 Increasing_frequency 2 +NC_045512.2 11527 11529 Positive_selection 2 +NC_045512.2 11527 11529 Unexpected_residues 2 +NC_045512.2 11533 11535 Positive_selection 2 +NC_045512.2 11533 11535 Multiple_Clades 2 +NC_045512.2 12331 12333 Negative_selection 1 +NC_045512.2 13512 13514 Positive_selection 3 +NC_045512.2 13512 13514 Multiple_Clades 3 +NC_045512.2 13512 13514 Unexpected_residues 3 +NC_045512.2 13626 13628 Positive_selection 3 +NC_045512.2 13626 13628 Increasing_frequency 3 +NC_045512.2 13626 13628 Intra-host_variants 3 +NC_045512.2 13728 13730 Positive_selection 5 +NC_045512.2 13728 13730 Multiple_Clades 5 +NC_045512.2 13728 13730 Increasing_frequency 5 +NC_045512.2 13728 13730 Unexpected_residues 5 +NC_045512.2 13728 13730 Intra-host_variants 5 +NC_045512.2 13944 13946 Negative_selection 1 +NC_045512.2 14193 14195 Positive_selection 2 +NC_045512.2 14193 14195 Intra-host_variants 2 +NC_045512.2 14406 14408 Positive_selection 6 +NC_045512.2 14406 14408 Multiple_Clades 6 +NC_045512.2 14406 14408 Common_Variant 6 +NC_045512.2 14406 14408 Increasing_frequency 6 +NC_045512.2 14406 14408 Unexpected_residues 6 +NC_045512.2 14406 14408 Intra-host_variants 6 +NC_045512.2 15276 15278 Positive_selection 3 +NC_045512.2 15276 15278 Increasing_frequency 3 +NC_045512.2 15276 15278 Intra-host_variants 3 +NC_045512.2 15705 15707 Negative_selection 1 +NC_045512.2 16533 16535 Positive_selection 1 +NC_045512.2 17124 17126 Positive_selection 2 +NC_045512.2 17124 17126 Increasing_frequency 2 +NC_045512.2 17244 17246 Negative_selection 1 +NC_045512.2 17277 17279 Positive_selection 2 +NC_045512.2 17277 17279 Unexpected_residues 2 +NC_045512.2 17409 17411 Positive_selection 2 +NC_045512.2 17409 17411 Multiple_Clades 2 +NC_045512.2 17472 17474 Positive_selection 1 +NC_045512.2 17796 17798 Negative_selection 1 +NC_045512.2 17823 17825 Positive_selection 3 +NC_045512.2 17823 17825 Unexpected_residues 3 +NC_045512.2 17823 17825 Intra-host_variants 3 +NC_045512.2 17883 17885 Positive_selection 1 +NC_045512.2 18651 18653 Positive_selection 2 +NC_045512.2 18651 18653 Intra-host_variants 2 +NC_045512.2 18654 18656 Positive_selection 1 +NC_045512.2 18684 18686 Positive_selection 2 +NC_045512.2 18684 18686 Intra-host_variants 2 +NC_045512.2 19482 19484 Positive_selection 2 +NC_045512.2 19482 19484 Multiple_Clades 2 +NC_045512.2 21135 21137 Positive_selection 4 +NC_045512.2 21135 21137 Multiple_Clades 4 +NC_045512.2 21135 21137 Unexpected_residues 4 +NC_045512.2 21135 21137 Intra-host_variants 4 +NC_045512.2 21240 21242 Positive_selection 1 +NC_045512.2 21303 21305 Positive_selection 1 +NC_045512.2 28861 28863 New 4 +NC_045512.2 24931 24933 New 3 +NC_045512.2 25710 25712 New 3 +NC_045512.2 6721 6723 New 3 +NC_045512.2 9436 9438 New 3 +NC_045512.2 17823 17825 New 3 +NC_045512.2 21709 21711 New 2 +NC_045512.2 24094 24096 New 2 +NC_045512.2 29302 29304 New 2 +NC_045512.2 25503 25505 New 2 +NC_045512.2 25944 25946 New 2 +NC_045512.2 6253 6255 New 2 +NC_045512.2 14193 14195 New 2 +NC_045512.2 17409 17411 New 2 +NC_045512.2 19482 19484 New 2 +NC_045512.2 29413 29415 New 1 +NC_045512.2 26780 26782 New 1 +NC_045512.2 25467 25469 New 1 +NC_045512.2 25605 25607 New 1 +NC_045512.2 26028 26030 New 1 +NC_045512.2 26043 26045 New 1 +NC_045512.2 26106 26108 New 1 +NC_045512.2 26196 26198 New 1 +NC_045512.2 10333 10335 New 1 +NC_045512.2 21303 21305 New 1 diff --git a/genomics/4-Variation/selection_analysis_ucsc.bed b/genomics/4-Variation/selection_analysis_ucsc.bed new file mode 100644 index 00000000..66402ec6 --- /dev/null +++ b/genomics/4-Variation/selection_analysis_ucsc.bed @@ -0,0 +1,307 @@ +NC_045512v2 21583 21585 Positive_selection 1 +NC_045512v2 21646 21648 Positive_selection 1 +NC_045512v2 21709 21711 Positive_selection 2 +NC_045512v2 21709 21711 Intra-host_variants 2 +NC_045512v2 21787 21789 Positive_selection 1 +NC_045512v2 21829 21831 Positive_selection 1 +NC_045512v2 21844 21846 Positive_selection 1 +NC_045512v2 21988 21990 Positive_selection 2 +NC_045512v2 21988 21990 Unexpected_residues 2 +NC_045512v2 21994 21996 Positive_selection 2 +NC_045512v2 21994 21996 Intra-host_variants 2 +NC_045512v2 22660 22662 Positive_selection 3 +NC_045512v2 22660 22662 Multiple_Clades 3 +NC_045512v2 22660 22662 Intra-host_variants 3 +NC_045512v2 22876 22878 Positive_selection 1 +NC_045512v2 23401 23403 Common_Variant 2 +NC_045512v2 23401 23403 Increasing_frequency 2 +NC_045512v2 23404 23406 Positive_selection 2 +NC_045512v2 23404 23406 Unexpected_residues 2 +NC_045512v2 23677 23679 Positive_selection 1 +NC_045512v2 24052 24054 Positive_selection 2 +NC_045512v2 24052 24054 Increasing_frequency 2 +NC_045512v2 24094 24096 Positive_selection 2 +NC_045512v2 24094 24096 Intra-host_variants 2 +NC_045512v2 24388 24390 Positive_selection 2 +NC_045512v2 24388 24390 Multiple_Clades 2 +NC_045512v2 24679 24681 Positive_selection 2 +NC_045512v2 24679 24681 Unexpected_residues 2 +NC_045512v2 24931 24933 Positive_selection 3 +NC_045512v2 24931 24933 Multiple_Clades 3 +NC_045512v2 24931 24933 Unexpected_residues 3 +NC_045512v2 28309 28311 Positive_selection 4 +NC_045512v2 28309 28311 Multiple_Clades 4 +NC_045512v2 28309 28311 Increasing_frequency 4 +NC_045512v2 28309 28311 Intra-host_variants 4 +NC_045512v2 28330 28332 Positive_selection 1 +NC_045512v2 28336 28338 Positive_selection 2 +NC_045512v2 28336 28338 Increasing_frequency 2 +NC_045512v2 28372 28374 Positive_selection 3 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Multiple_Clades 3 +NC_045512v2 6634 6636 Intra-host_variants 3 +NC_045512v2 6694 6696 Positive_selection 2 +NC_045512v2 6694 6696 Multiple_Clades 2 +NC_045512v2 6721 6723 Positive_selection 3 +NC_045512v2 6721 6723 Multiple_Clades 3 +NC_045512v2 6721 6723 Increasing_frequency 3 +NC_045512v2 6988 6990 Positive_selection 3 +NC_045512v2 6988 6990 Multiple_Clades 3 +NC_045512v2 6988 6990 Increasing_frequency 3 +NC_045512v2 7009 7011 Positive_selection 3 +NC_045512v2 7009 7011 Multiple_Clades 3 +NC_045512v2 7009 7011 Increasing_frequency 3 +NC_045512v2 7987 7989 Negative_selection 1 +NC_045512v2 8779 8781 Negative_selection 2 +NC_045512v2 8779 8781 Intra-host_variants 2 +NC_045512v2 8788 8790 Positive_selection 2 +NC_045512v2 8788 8790 Multiple_Clades 2 +NC_045512v2 9109 9111 Positive_selection 1 +NC_045512v2 9436 9438 Positive_selection 3 +NC_045512v2 9436 9438 Multiple_Clades 3 +NC_045512v2 9436 9438 Intra-host_variants 3 +NC_045512v2 10321 10323 Positive_selection 4 +NC_045512v2 10321 10323 Multiple_Clades 4 +NC_045512v2 10321 10323 Increasing_frequency 4 +NC_045512v2 10321 10323 Intra-host_variants 4 +NC_045512v2 10333 10335 Positive_selection 1 +NC_045512v2 10711 10713 Positive_selection 1 +NC_045512v2 11071 11073 Negative_selection 2 +NC_045512v2 11071 11073 Intra-host_variants 2 +NC_045512v2 11080 11082 Positive_selection 2 +NC_045512v2 11080 11082 Intra-host_variants 2 +NC_045512v2 11404 11406 Positive_selection 2 +NC_045512v2 11404 11406 Increasing_frequency 2 +NC_045512v2 11527 11529 Positive_selection 2 +NC_045512v2 11527 11529 Unexpected_residues 2 +NC_045512v2 11533 11535 Positive_selection 2 +NC_045512v2 11533 11535 Multiple_Clades 2 +NC_045512v2 12331 12333 Negative_selection 1 +NC_045512v2 13512 13514 Positive_selection 3 +NC_045512v2 13512 13514 Multiple_Clades 3 +NC_045512v2 13512 13514 Unexpected_residues 3 +NC_045512v2 13626 13628 Positive_selection 3 +NC_045512v2 13626 13628 Increasing_frequency 3 +NC_045512v2 13626 13628 Intra-host_variants 3 +NC_045512v2 13728 13730 Positive_selection 5 +NC_045512v2 13728 13730 Multiple_Clades 5 +NC_045512v2 13728 13730 Increasing_frequency 5 +NC_045512v2 13728 13730 Unexpected_residues 5 +NC_045512v2 13728 13730 Intra-host_variants 5 +NC_045512v2 13944 13946 Negative_selection 1 +NC_045512v2 14193 14195 Positive_selection 2 +NC_045512v2 14193 14195 Intra-host_variants 2 +NC_045512v2 14406 14408 Positive_selection 6 +NC_045512v2 14406 14408 Multiple_Clades 6 +NC_045512v2 14406 14408 Common_Variant 6 +NC_045512v2 14406 14408 Increasing_frequency 6 +NC_045512v2 14406 14408 Unexpected_residues 6 +NC_045512v2 14406 14408 Intra-host_variants 6 +NC_045512v2 15276 15278 Positive_selection 3 +NC_045512v2 15276 15278 Increasing_frequency 3 +NC_045512v2 15276 15278 Intra-host_variants 3 +NC_045512v2 15705 15707 Negative_selection 1 +NC_045512v2 16533 16535 Positive_selection 1 +NC_045512v2 17124 17126 Positive_selection 2 +NC_045512v2 17124 17126 Increasing_frequency 2 +NC_045512v2 17244 17246 Negative_selection 1 +NC_045512v2 17277 17279 Positive_selection 2 +NC_045512v2 17277 17279 Unexpected_residues 2 +NC_045512v2 17409 17411 Positive_selection 2 +NC_045512v2 17409 17411 Multiple_Clades 2 +NC_045512v2 17472 17474 Positive_selection 1 +NC_045512v2 17796 17798 Negative_selection 1 +NC_045512v2 17823 17825 Positive_selection 3 +NC_045512v2 17823 17825 Unexpected_residues 3 +NC_045512v2 17823 17825 Intra-host_variants 3 +NC_045512v2 17883 17885 Positive_selection 1 +NC_045512v2 18651 18653 Positive_selection 2 +NC_045512v2 18651 18653 Intra-host_variants 2 +NC_045512v2 18654 18656 Positive_selection 1 +NC_045512v2 18684 18686 Positive_selection 2 +NC_045512v2 18684 18686 Intra-host_variants 2 +NC_045512v2 19482 19484 Positive_selection 2 +NC_045512v2 19482 19484 Multiple_Clades 2 +NC_045512v2 21135 21137 Positive_selection 4 +NC_045512v2 21135 21137 Multiple_Clades 4 +NC_045512v2 21135 21137 Unexpected_residues 4 +NC_045512v2 21135 21137 Intra-host_variants 4 +NC_045512v2 21240 21242 Positive_selection 1 +NC_045512v2 21303 21305 Positive_selection 1 +NC_045512v2 28861 28863 New 4 +NC_045512v2 24931 24933 New 3 +NC_045512v2 25710 25712 New 3 +NC_045512v2 6721 6723 New 3 +NC_045512v2 9436 9438 New 3 +NC_045512v2 17823 17825 New 3 +NC_045512v2 21709 21711 New 2 +NC_045512v2 24094 24096 New 2 +NC_045512v2 29302 29304 New 2 +NC_045512v2 25503 25505 New 2 +NC_045512v2 25944 25946 New 2 +NC_045512v2 6253 6255 New 2 +NC_045512v2 14193 14195 New 2 +NC_045512v2 17409 17411 New 2 +NC_045512v2 19482 19484 New 2 +NC_045512v2 29413 29415 New 1 +NC_045512v2 26780 26782 New 1 +NC_045512v2 25467 25469 New 1 +NC_045512v2 25605 25607 New 1 +NC_045512v2 26028 26030 New 1 +NC_045512v2 26043 26045 New 1 +NC_045512v2 26106 26108 New 1 +NC_045512v2 26196 26198 New 1 +NC_045512v2 10333 10335 New 1 +NC_045512v2 21303 21305 New 1 diff --git a/genomics/4-Variation/selection_summary_to_bed.py b/genomics/4-Variation/selection_summary_to_bed.py new file mode 100644 index 00000000..ee70fd95 --- /dev/null +++ b/genomics/4-Variation/selection_summary_to_bed.py @@ -0,0 +1,24 @@ +"""Takes a dump of the selection summary from https://observablehq.com/@spond/natural-selection-analysis-of-sars-cov-2-covid-19 and turns it into a bed file.""" +import json + +import pandas as pd + + +CHROMS = [('ncbi', 'NC_045512.2'), ('ucsc', 'NC_045512v2')] + + +with open('summary.json') as fh: + summary = json.load(fh) + +df = pd.DataFrame.from_records(summary['plot']) +# Neither IGV nor UCSC support spaces in the name field +df['kind'] = df['kind'].str.replace(' ', '_') +df['start'] = df['position'] -1 +df['end'] = df['start'] + 2 +df['strand'] = '+' + +for (convention, chrom) in CHROMS: + df['chrom'] = chrom + df[['chrom', 'start', 'end', 'kind', 'score']].to_csv( + "selection_analysis_%s.bed" % convention, sep='\t', index=None, header=None, + ) diff --git a/genomics/4-Variation/summary.json b/genomics/4-Variation/summary.json new file mode 100644 index 00000000..4065489a --- /dev/null +++ b/genomics/4-Variation/summary.json @@ -0,0 +1 @@ +{"table":[{"site":"ORF1b 313
RdRp 323
Genomic 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Genomic 28254-28256","classification":{"fel":true,"meme":true,"fraction":0.1108362499779386,"kind":"positive","branches":2,"evo_support":false},"substitutions":[1,3],"variants":[],"composition":{"composition":"I10586S3L2","variants":[]},"score":3,"for_plot":{"position":28254,"gene":"ORF8","site_in_gene":121,"kind":"Unexpected residues","score":3},"prior":[["20200330","20200410","20200412","20200414","20200415","20200418"],10]},{"site":"ORF1a 580
nsp2 400
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nsp2 480
Genomic 2243-2245","classification":{"fel":true,"meme":true,"fraction":0.9923351401090127,"kind":"positive","branches":1,"evo_support":false,"variants":1},"substitutions":[0,1],"variants":[["ORF1a",660,0.069231,2247,"gGt/gTt","NON_SYNONYMOUS_CODING","SRR11494646"]],"composition":{"composition":"V8502A7","variants":[["ORF1a",660,0.069231,2247,"gGt/gTt","NON_SYNONYMOUS_CODING","SRR11494646"]]},"score":3,"for_plot":{"position":2243,"gene":"ORF1a","site_in_gene":660,"peptide":"nsp2 480","kind":"Intra-host variants","score":3},"prior":[["20200414","20200415","20200418"],10]},{"site":"ORF1a 924
nsp3 106
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106","kind":"Intra-host variants","score":3},"prior":[["20200325","20200330","20200404","20200408","20200410","20200412","20200414","20200415","20200418"],10]},{"site":"ORF1a 1036
nsp3 218
Genomic 3371-3373","classification":{"fel":true,"meme":true,"fraction":0.9921948092065762,"kind":"positive","branches":1,"trend":true,"evo_support":true,"variants":4},"substitutions":[0,1],"variants":[["ORF1a",1036,0.986395,3373,"gaC/gaA","NON_SYNONYMOUS_CODING","SRR11494544"],["ORF1a",1036,0.9585799999999999,3373,"gaC/gaA","NON_SYNONYMOUS_CODING","SRR11494510"],["ORF1a",1036,0.955224,3373,"gaC/gaA","NON_SYNONYMOUS_CODING","SRR11494657"],["ORF1a",1036,0.923077,3373,"gaC/gaA","NON_SYNONYMOUS_CODING","SRR11494552"]],"composition":{"composition":"D8473","variants":[["ORF1a",1036,0.986395,3373,"gaC/gaA","NON_SYNONYMOUS_CODING","SRR11494544"],["ORF1a",1036,0.9585799999999999,3373,"gaC/gaA","NON_SYNONYMOUS_CODING","SRR11494510"],["ORF1a",1036,0.955224,3373,"gaC/gaA","NON_SYNONYMOUS_CODING","SRR11494657"],["ORF1a",1036,0.923077,3373,"gaC/gaA","NON_SYNONYMOUS_CODING","SRR11494552"]]},"score":3,"for_plot":{"position":3371,"gene":"ORF1a","site_in_gene":1036,"peptide":"nsp3 218","kind":"Intra-host variants","score":3},"prior":[["20200325","20200330","20200403","20200404","20200408","20200410","20200412","20200414","20200415","20200418"],10]},{"site":"ORF1a 2016
nsp3 1198
Genomic 6311-6313","classification":{"fel":true,"meme":false,"fraction":0.4991162747930498,"kind":"positive","branches":2,"trend":true,"evo_support":true},"substitutions":[0,2],"variants":[],"composition":{"composition":"T8453I3","variants":[]},"score":3,"for_plot":{"position":6311,"gene":"ORF1a","site_in_gene":2016,"peptide":"nsp3 1198","kind":"Increasing frequency","score":3},"prior":[["20200415","20200418"],10]},{"site":"ORF1a 2124
nsp3 1306
Genomic 6635-6637","classification":{"fel":true,"meme":true,"fraction":0.9967682264068324,"kind":"positive","branches":2,"evo_support":true,"variants":2},"substitutions":[0,2],"variants":[["ORF1a",2124,0.981982,6638,"Cat/Tat","NON_SYNONYMOUS_CODING","SRR11494587"],["ORF1a",2124,0.9639639999999999,6638,"Cat/Tat","NON_SYNONYMOUS_CODING","SRR11494751"]],"composition":{"composition":"T8502I6","variants":[["ORF1a",2124,0.981982,6638,"Cat/Tat","NON_SYNONYMOUS_CODING","SRR11494587"],["ORF1a",2124,0.9639639999999999,6638,"Cat/Tat","NON_SYNONYMOUS_CODING","SRR11494751"]]},"score":3,"for_plot":{"position":6635,"gene":"ORF1a","site_in_gene":2124,"peptide":"nsp3 1306","kind":"Intra-host variants","score":3},"prior":[["20200415","20200418"],10]},{"site":"ORF1a 2153
nsp3 1335
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nsp4 79
Genomic 8789-8791","classification":{"fel":true,"meme":true,"fraction":0.9983764965936973,"kind":"positive","branches":2,"evo_support":true},"substitutions":[0,2],"variants":[],"composition":{"composition":"G8490V15","variants":[]},"score":2,"for_plot":{"position":8789,"gene":"ORF1a","site_in_gene":2842,"peptide":"nsp4 79","kind":"Multiple Clades","score":2},"prior":[["20200418"],10]},{"site":"ORF1a 3603
nsp6 34
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