FL-4 - Complete Raw Mutation Data

Full TSV data with all sample columns and abundance information
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Complete Mutations Data

This table shows the complete data from the mutations.tsv file exactly as it appears in the source. Scroll horizontally to see all columns.

SRR33584290(5649751) SRR33584297(9794902) SRR33614833(3680378) SRR33614837(4739098) SRR33614838(4399372) SRR33614891(3657134) SRR33614892(3992250) SRR33694414(6005028)
('2025-05-07', '776150') ('2025-05-06', '212065') ('2025-05-11', '750000') ('2025-05-11', '59587') ('2025-05-11', '80000') ('2025-05-11', '463672') ('2025-05-11', '277823') ('2025-05-11', '212065')
Sequences Count Abundance Count Abundance Count Abundance Count Abundance Count Abundance Count Abundance Count Abundance Count Abundance Total samples Positives Sum Negatives Sum Total Sum
77 T77A 1 0.010 1 0.01 0 0.01
190 C190G 935 0.006 1 0.000 1 0.000 3 0.006 0.0 0.006
190 RATG13 C190T 122581 0.741 1 0.000 2 0.000 2 0.000 1 0.000 5 0.741 0.0 0.741
196 196-insertAC 120782 0.730 1 0.73 0 0.73
197 197-insertCT 749 0.005 1 0.005 0 0.005
199 G199A 122356 0.737 1 0.000 1 0.000 3 0.737 0.0 0.737
201 T201G 122944 0.740 6 0.001 19 0.001 22 0.001 13 0.001 20 0.000 6 0.74 0.004 0.744
212 T212C 123355 0.742 7 0.000 6 0.000 2 0.000 4 0.742 0.0 0.742
218 C218A 1509 0.009 4 0.000 2 0.000 2 0.000 9 0.000 5 0.009 0.0 0.009
222 C222A 123092 0.740 2 0.000 9 0.000 12 0.000 7 0.000 35 0.001 6 0.74 0.001 0.741
425 GTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTT425-457del|(ORF1ab_polyprotein:160-192del(VEVEKGVLPQL54-64del))|(ORF1a_polyprotein:160-192del(VEVEKGVLPQL54-64del)) 626 0.725 1 0.725 0 0.725
442 C442A|(ORF1ab_polyprotein:C177A(G59G))|(ORF1a_polyprotein:C177A(G59G)) 124 0.116 1 0.012 2 0.116 0.012 0.128
444 444-insertA|(ORF1ab_polyprotein:179insertA(60fs))|(ORF1a_polyprotein:179insertA(60fs)) 140 0.125 1 0.125 0 0.125
446 T446A|(ORF1ab_polyprotein:T181A(L61M))|(ORF1a_polyprotein:T181A(L61M)) 149 0.173 1 0.173 0 0.173
451 T451G|(ORF1ab_polyprotein:T186G(P62P))|(ORF1a_polyprotein:T186G(P62P)) 111334 0.992 1 0.992 0 0.992
465 C465A|(ORF1ab_polyprotein:C200A(P67H))|(ORF1a_polyprotein:C200A(P67H)) 632 0.006 1 0.006 0 0.006
linked 474 T474C|(ORF1ab_polyprotein:T209C(F70S))|(ORF1a_polyprotein:T209C(F70S)) 286 0.003 1 0.003 0 0.003
486 C486T|(ORF1ab_polyprotein:C221T(S74L))|(ORF1a_polyprotein:C221T(S74L)) 625 0.006 1 0.006 0 0.006
487 RATG13 G487T|(ORF1ab_polyprotein:G222T(S74S))|(ORF1a_polyprotein:G222T(S74S)) 555 0.005 1 0.005 0 0.005
508 T508-508del|(ORF1ab_polyprotein:243-243del(81fs))|(ORF1a_polyprotein:243-243del(81fs)) 66 0.082 1 0.082 0 0.082
508 TGGTCATGTT508-517del|(ORF1ab_polyprotein:CATGGTCATGTTATGGTT241-258CAAdel(HGHVMV81-86Qdel))|(ORF1a_polyprotein:CATGGTCATGTTATGGTT241-258CAAdel(HGHVMV81-86Qdel)) 271 0.403 1 0.403 0 0.403
linked 508 TGGTCATGTTATGGT508-522del|(ORF1ab_polyprotein:CATGGTCATGTTATGGTT241-258CATdel(HGHVMV81-86Hdel))|(ORF1a_polyprotein:CATGGTCATGTTATGGTT241-258CATdel(HGHVMV81-86Hdel)) 357 0.530 11 0.133 1 0.011 32 0.262 4 0.53 0.406 0.936
519 TGGTT519-523del|(ORF1ab_polyprotein:CATGGTCATGTTATGGTT241-258CAAdel(HGHVMV81-86Qdel))|(ORF1a_polyprotein:CATGGTCATGTTATGGTT241-258CAAdel(HGHVMV81-86Qdel)) 271 0.403 1 0.403 0 0.403
560 C560A|(ORF1ab_polyprotein:C295A(R99S))|(ORF1a_polyprotein:C295A(R99S)) 629 0.932 1 0.932 0 0.932
593 RATG13 C593T|(ORF1ab_polyprotein:CAT328-330TAC(H110Y))|(ORF1a_polyprotein:CAT328-330TAC(H110Y)) 629 0.932 1 0.932 0 0.932
595 T595C|(ORF1ab_polyprotein:CAT328-330TAC(H110Y))|(ORF1a_polyprotein:CAT328-330TAC(H110Y)) 629 0.932 1 0.932 0 0.932
632 C632T|(ORF1ab_polyprotein:C367T(L123F))|(ORF1a_polyprotein:C367T(L123F)) 623 0.931 1 0.931 0 0.931
636 G636T|(ORF1ab_polyprotein:CGT370-372CTC(R124L))|(ORF1a_polyprotein:CGT370-372CTC(R124L)) 4 0.006 1 0.006 0 0.006
637 T637C|(ORF1ab_polyprotein:CGT370-372CTC(R124L))|(ORF1a_polyprotein:CGT370-372CTC(R124L)) 4 0.006 1 0.006 0 0.006
637 T637C|(ORF1ab_polyprotein:T372C(R124R))|(ORF1a_polyprotein:T372C(R124R)) 621 0.925 1 0.925 0 0.925
639 A639C|(ORF1ab_polyprotein:A374C(K125T))|(ORF1a_polyprotein:A374C(K125T)) 6 0.009 1 0.009 0 0.009
649 T649A|(ORF1ab_polyprotein:T384A(N128K))|(ORF1a_polyprotein:T384A(N128K)) 475 0.854 1 0.854 0 0.854
653 G653A|(ORF1ab_polyprotein:G388A(G130R))|(ORF1a_polyprotein:G388A(G130R)) 268 0.476 1 0.476 0 0.476
670 T670A|(ORF1ab_polyprotein:T405A(S135R))|(ORF1a_polyprotein:T405A(S135R)) 473 0.624 1 0.624 0 0.624
linked 684 T684C|(ORF1ab_polyprotein:T419C(L140P))|(ORF1a_polyprotein:T419C(L140P)) 530 0.002 4 0.000 5 0.000 5 0.000 3 0.000 12 0.000 15 0.000 7 0.002 0.0 0.002
linkedubiq 897 C897A|(ORF1ab_polyprotein:C632A(A211D))|(ORF1a_polyprotein:C632A(A211D)) 277252 0.995 54710 0.997 54794 0.996 9792 0.273 56695 0.808 51117 0.676 251921 0.996 7 0.995 4.746 5.7410000000000005
900 C900T|(ORF1ab_polyprotein:C635T(S212L))|(ORF1a_polyprotein:C635T(S212L)) 98069 0.352 3 0.000 6 0.000 2 0.000 9 0.000 3 0.000 9 0.000 7 0.352 0.0 0.352
936 C936T|(ORF1ab_polyprotein:C671T(T224I))|(ORF1a_polyprotein:C671T(T224I)) 60970 0.219 1 0.000 1 0.000 1 0.000 2 0.000 6 0.000 6 0.219 0.0 0.219
1123 A1123T|(ORF1ab_polyprotein:A858T(P286P))|(ORF1a_polyprotein:A858T(P286P)) 12 0.005 5 0.000 5 0.000 1 0.000 3 0.000 5 0.005 0.0 0.005
1139 A1139C|(ORF1ab_polyprotein:A874C(K292Q))|(ORF1a_polyprotein:A874C(K292Q)) 12 0.005 6 0.000 2 0.000 3 0.005 0.0 0.005
1354 T1354A|(ORF1ab_polyprotein:T1089A(N363K))|(ORF1a_polyprotein:T1089A(N363K)) 2 0.007 1 0.007 0 0.007
1385 C1385T|(ORF1ab_polyprotein:C1120T(H374Y))|(ORF1a_polyprotein:C1120T(H374Y)) 2 0.007 1 0.007 0 0.007
1394 G1394T|(ORF1ab_polyprotein:G1129T(E377*))|(ORF1a_polyprotein:G1129T(E377*)) 2 0.007 1 0.007 0 0.007
1439 G1439T|(ORF1ab_polyprotein:G1174T(G392C))|(ORF1a_polyprotein:G1174T(G392C)) 3 0.010 1 0.01 0 0.01
1443 T1443A|(ORF1ab_polyprotein:T1178A(L393*))|(ORF1a_polyprotein:T1178A(L393*)) 2 0.007 1 0.007 0 0.007
1451 A1451T|(ORF1ab_polyprotein:A1186T(I396F))|(ORF1a_polyprotein:A1186T(I396F)) 2 0.007 1 0.007 0 0.007
1465 T1465A|(ORF1ab_polyprotein:T1200A(G400G))|(ORF1a_polyprotein:T1200A(G400G)) 2 0.007 1 0.007 0 0.007
1473 C1473A|(ORF1ab_polyprotein:C1208A(T403N))|(ORF1a_polyprotein:C1208A(T403N)) 2 0.007 1 0.007 0 0.007
1513 C1513A|(ORF1ab_polyprotein:C1248A(C416*))|(ORF1a_polyprotein:C1248A(C416*)) 3 0.010 1 0.01 0 0.01
1528 C1528A|(ORF1ab_polyprotein:C1263A(A421A))|(ORF1a_polyprotein:C1263A(A421A)) 2 0.007 1 0.007 0 0.007
1571 A1571T|(ORF1ab_polyprotein:A1306T(T436S))|(ORF1a_polyprotein:A1306T(T436S)) 2 0.007 1 0.007 0 0.007
1571 A1571T|(ORF1ab_polyprotein:ACA1306-1308TGA(T436*))|(ORF1a_polyprotein:ACA1306-1308TGA(T436*)) 2 0.007 1 0.007 0 0.007
1572 C1572G|(ORF1ab_polyprotein:ACA1306-1308TGA(T436*))|(ORF1a_polyprotein:ACA1306-1308TGA(T436*)) 2 0.007 1 0.007 0 0.007
1598 G1598T|(ORF1ab_polyprotein:G1333T(G445C))|(ORF1a_polyprotein:G1333T(G445C)) 2 0.007 1 0.007 0 0.007
ubiq 1758 C1758T|(ORF1ab_polyprotein:C1493T(A498V))|(ORF1a_polyprotein:C1493T(A498V)) 46021 0.991 7 0.000 9 0.000 22748 0.308 4 0.991 0.308 1.299
ubiq 1954 G1954A|(ORF1ab_polyprotein:G1689A(Q563Q))|(ORF1a_polyprotein:G1689A(Q563Q)) 100275 0.998 12793 0.999 21051 0.554 13119 0.452 1 0.000 6666 0.999 6 0.998 3.004 4.002
2256 T2256A|(ORF1ab_polyprotein:T1991A(I664N))|(ORF1a_polyprotein:T1991A(I664N)) 1 0.012 1 0.012 0 0.012
2256 T2256G|(ORF1ab_polyprotein:T1991G(I664S))|(ORF1a_polyprotein:T1991G(I664S)) 1 0.012 1 0.012 0 0.012
2257 2257-insertG|(ORF1ab_polyprotein:1992insertG(664fs))|(ORF1a_polyprotein:1992insertG(664fs)) 1 0.012 1 0.012 0 0.012
2258 G2258T|(ORF1ab_polyprotein:G1993T(V665F))|(ORF1a_polyprotein:G1993T(V665F)) 1 0.012 1 0.012 0 0.012
ubiq 2790 C2790T|(ORF1ab_polyprotein:C2525T(T842I))|(ORF1a_polyprotein:C2525T(T842I)) 1863 0.995 4273 0.998 5361 0.996 37189 0.998 29059 0.997 10555 0.997 6 0.995 4.986 5.981
ubiq 3037 RATG13,Delta C3037T|(ORF1ab_polyprotein:C2772T(F924F))|(ORF1a_polyprotein:C2772T(F924F)) 9738 0.991 3864 0.992 7170 0.988 2673 0.991 3745 0.993 1352 0.992 16552 0.993 7 0.991 5.949 6.9399999999999995
3096 C3096T|(ORF1ab_polyprotein:C2831T(S944L))|(ORF1a_polyprotein:C2831T(S944L)) 63 0.006 1 0.000 1 0.000 3 0.006 0.0 0.006
3231 RATG13 G3231T|(ORF1ab_polyprotein:G2966T(G989V))|(ORF1a_polyprotein:G2966T(G989V)) 1 0.008 1 0.008 0 0.008
3236 C3236A|(ORF1ab_polyprotein:C2971A(Q991K))|(ORF1a_polyprotein:C2971A(Q991K)) 1 0.008 1 0.008 0 0.008
3244 C3244A|(ORF1ab_polyprotein:C2979A(G993G))|(ORF1a_polyprotein:C2979A(G993G)) 1 0.008 1 0.008 0 0.008
3248 G3248T|(ORF1ab_polyprotein:G2983T(E995*))|(ORF1a_polyprotein:G2983T(E995*)) 1 0.008 1 0.008 0 0.008
3251 G3251T|(ORF1ab_polyprotein:G2986T(D996Y))|(ORF1a_polyprotein:G2986T(D996Y)) 2 0.016 1 0.016 0 0.016
3256 T3256A|(ORF1ab_polyprotein:T2991A(N997K))|(ORF1a_polyprotein:T2991A(N997K)) 2 0.016 1 0.016 0 0.016
3265 T3265A|(ORF1ab_polyprotein:T3000A(T1000T))|(ORF1a_polyprotein:T3000A(T1000T)) 1 0.008 1 0.008 0 0.008
3267 C3267A|(ORF1ab_polyprotein:C3002A(T1001N))|(ORF1a_polyprotein:C3002A(T1001N)) 2 0.016 1 0.016 0 0.016
3268 T3268A|(ORF1ab_polyprotein:T3003A(T1001T))|(ORF1a_polyprotein:T3003A(T1001T)) 2 0.016 1 0.016 0 0.016
3271 T3271A|(ORF1ab_polyprotein:T3006A(I1002I))|(ORF1a_polyprotein:T3006A(I1002I)) 1 0.008 1 0.008 0 0.008
3278 A3278T|(ORF1ab_polyprotein:A3013T(I1005F))|(ORF1a_polyprotein:A3013T(I1005F)) 1 0.008 1 0.008 0 0.008
3279 T3279A|(ORF1ab_polyprotein:T3014A(I1005N))|(ORF1a_polyprotein:T3014A(I1005N)) 2 0.016 1 0.016 0 0.016
3280 T3280G|(ORF1ab_polyprotein:T3015G(I1005M))|(ORF1a_polyprotein:T3015G(I1005M)) 1 0.008 1 0.008 0 0.008
3283 T3283A|(ORF1ab_polyprotein:T3018A(V1006V))|(ORF1a_polyprotein:T3018A(V1006V)) 3 0.025 1 0.025 0 0.025
3284 G3284C|(ORF1ab_polyprotein:G3019C(E1007Q))|(ORF1a_polyprotein:G3019C(E1007Q)) 1 0.008 1 0.008 0 0.008
3285 A3285G|(ORF1ab_polyprotein:A3020G(E1007G))|(ORF1a_polyprotein:A3020G(E1007G)) 1 0.008 1 0.008 0 0.008
3294 C3294A|(ORF1ab_polyprotein:C3029A(P1010H))|(ORF1a_polyprotein:C3029A(P1010H)) 2 0.016 1 0.016 0 0.016
3299 T3299A|(ORF1ab_polyprotein:T3034A(L1012I))|(ORF1a_polyprotein:T3034A(L1012I)) 2 0.016 1 0.016 0 0.016
3300 T3300A|(ORF1ab_polyprotein:T3035A(L1012*))|(ORF1a_polyprotein:T3035A(L1012*)) 1 0.008 1 0.008 0 0.008
3301 A3301C|(ORF1ab_polyprotein:A3036C(L1012F))|(ORF1a_polyprotein:A3036C(L1012F)) 1 0.008 1 0.008 0 0.008
3303 A3303T|(ORF1ab_polyprotein:A3038T(E1013V))|(ORF1a_polyprotein:A3038T(E1013V)) 1 0.008 1 0.008 0 0.008
3305 A3305C|(ORF1ab_polyprotein:A3040C(M1014L))|(ORF1a_polyprotein:A3040C(M1014L)) 1 0.008 1 0.008 0 0.008
3306 T3306A|(ORF1ab_polyprotein:T3041A(M1014K))|(ORF1a_polyprotein:T3041A(M1014K)) 1 0.008 1 0.008 0 0.008
3310 A3310C|(ORF1ab_polyprotein:A3045C(E1015D))|(ORF1a_polyprotein:A3045C(E1015D)) 1 0.008 1 0.008 0 0.008
3311 C3311G|(ORF1ab_polyprotein:C3046G(L1016V))|(ORF1a_polyprotein:C3046G(L1016V)) 1 0.008 1 0.008 0 0.008
3312 T3312A|(ORF1ab_polyprotein:T3047A(L1016H))|(ORF1a_polyprotein:T3047A(L1016H)) 1 0.008 1 0.008 0 0.008
3317 C3317A|(ORF1ab_polyprotein:C3052A(P1018T))|(ORF1a_polyprotein:C3052A(P1018T)) 1 0.008 1 0.008 0 0.008
3322 T3322A|(ORF1ab_polyprotein:T3057A(V1019V))|(ORF1a_polyprotein:T3057A(V1019V)) 1 0.008 1 0.008 0 0.008
3330 C3330A|(ORF1ab_polyprotein:C3065A(T1022N))|(ORF1a_polyprotein:C3065A(T1022N)) 1 0.008 1 0.008 0 0.008
3333 T3333A|(ORF1ab_polyprotein:ATT3067-3069AAA(I1023K))|(ORF1a_polyprotein:ATT3067-3069AAA(I1023K)) 1 0.008 1 0.008 0 0.008
3334 T3334A|(ORF1ab_polyprotein:ATT3067-3069AAA(I1023K))|(ORF1a_polyprotein:ATT3067-3069AAA(I1023K)) 1 0.008 1 0.008 0 0.008
3334 T3334G|(ORF1ab_polyprotein:T3069G(I1023M))|(ORF1a_polyprotein:T3069G(I1023M)) 1 0.008 1 0.008 0 0.008
3338 G3338T|(ORF1ab_polyprotein:G3073T(V1025L))|(ORF1a_polyprotein:G3073T(V1025L)) 1 0.007 1 0.007 0 0.007
3342 A3342C|(ORF1ab_polyprotein:A3077C(N1026T))|(ORF1a_polyprotein:A3077C(N1026T)) 3 0.021 1 0.021 0 0.021
3342 A3342T|(ORF1ab_polyprotein:A3077T(N1026I))|(ORF1a_polyprotein:A3077T(N1026I)) 1 0.007 1 0.007 0 0.007
3343 T3343G|(ORF1ab_polyprotein:T3078G(N1026K))|(ORF1a_polyprotein:T3078G(N1026K)) 1 0.007 1 0.007 0 0.007
3346 T3346A|(ORF1ab_polyprotein:T3081A(S1027R))|(ORF1a_polyprotein:T3081A(S1027R)) 2 0.014 1 0.014 0 0.014
3346 T3346G|(ORF1ab_polyprotein:T3081G(S1027R))|(ORF1a_polyprotein:T3081G(S1027R)) 1 0.007 1 0.007 0 0.007
3347 T3347G|(ORF1ab_polyprotein:T3082G(F1028V))|(ORF1a_polyprotein:T3082G(F1028V)) 1 0.007 1 0.007 0 0.007
3350 A3350C|(ORF1ab_polyprotein:A3085C(S1029R))|(ORF1a_polyprotein:A3085C(S1029R)) 2 0.014 1 0.014 0 0.014
3354 G3354C|(ORF1ab_polyprotein:G3089C(G1030A))|(ORF1a_polyprotein:G3089C(G1030A)) 1 0.007 1 0.007 0 0.007
3354 G3354T|(ORF1ab_polyprotein:G3089T(G1030V))|(ORF1a_polyprotein:G3089T(G1030V)) 1 0.007 1 0.007 0 0.007
3358 T3358A|(ORF1ab_polyprotein:T3093A(Y1031*))|(ORF1a_polyprotein:T3093A(Y1031*)) 2 0.014 1 0.014 0 0.014
3359 T3359C|(ORF1ab_polyprotein:T3094C(L1032L))|(ORF1a_polyprotein:T3094C(L1032L)) 1 0.007 1 0.007 0 0.007
3360 T3360G|(ORF1ab_polyprotein:T3095G(L1032*))|(ORF1a_polyprotein:T3095G(L1032*)) 1 0.007 1 0.007 0 0.007
3362 A3362C|(ORF1ab_polyprotein:A3097C(K1033Q))|(ORF1a_polyprotein:A3097C(K1033Q)) 1 0.007 1 0.007 0 0.007
3364 A3364T|(ORF1ab_polyprotein:A3099T(K1033N))|(ORF1a_polyprotein:A3099T(K1033N)) 1 0.007 1 0.007 0 0.007
3365 C3365A|(ORF1ab_polyprotein:C3100A(L1034I))|(ORF1a_polyprotein:C3100A(L1034I)) 1 0.007 1 0.007 0 0.007
3368 A3368C|(ORF1ab_polyprotein:A3103C(T1035P))|(ORF1a_polyprotein:A3103C(T1035P)) 1 0.007 1 0.007 0 0.007
3372 A3372T|(ORF1ab_polyprotein:A3107T(D1036V))|(ORF1a_polyprotein:A3107T(D1036V)) 2 0.014 1 0.014 0 0.014
3374 A3374C|(ORF1ab_polyprotein:AAT3109-3111CCT(N1037P))|(ORF1a_polyprotein:AAT3109-3111CCT(N1037P)) 1 0.007 1 0.007 0 0.007
3375 A3375C|(ORF1ab_polyprotein:AAT3109-3111CCT(N1037P))|(ORF1a_polyprotein:AAT3109-3111CCT(N1037P)) 1 0.007 1 0.007 0 0.007
3375 A3375T|(ORF1ab_polyprotein:A3110T(N1037I))|(ORF1a_polyprotein:A3110T(N1037I)) 1 0.007 1 0.007 0 0.007
3378 T3378G|(ORF1ab_polyprotein:T3113G(V1038G))|(ORF1a_polyprotein:T3113G(V1038G)) 1 0.007 1 0.007 0 0.007
3380 T3380A|(ORF1ab_polyprotein:T3115A(Y1039N))|(ORF1a_polyprotein:T3115A(Y1039N)) 1 0.007 1 0.007 0 0.007
3381 A3381G|(ORF1ab_polyprotein:A3116G(Y1039C))|(ORF1a_polyprotein:A3116G(Y1039C)) 1 0.007 1 0.007 0 0.007
3381 A3381T|(ORF1ab_polyprotein:A3116T(Y1039F))|(ORF1a_polyprotein:A3116T(Y1039F)) 1 0.007 1 0.007 0 0.007
3384 T3384G|(ORF1ab_polyprotein:ATT3118-3120AGA(I1040R))|(ORF1a_polyprotein:ATT3118-3120AGA(I1040R)) 1 0.007 1 0.007 0 0.007
3385 T3385A|(ORF1ab_polyprotein:ATT3118-3120AGA(I1040R))|(ORF1a_polyprotein:ATT3118-3120AGA(I1040R)) 1 0.007 1 0.007 0 0.007
3385 T3385C|(ORF1ab_polyprotein:T3120C(I1040I))|(ORF1a_polyprotein:T3120C(I1040I)) 1 0.007 1 0.007 0 0.007
3387 A3387C|(ORF1ab_polyprotein:A3122C(K1041T))|(ORF1a_polyprotein:A3122C(K1041T)) 1 0.007 1 0.007 0 0.007
3389 A3389C|(ORF1ab_polyprotein:A3124C(N1042H))|(ORF1a_polyprotein:A3124C(N1042H)) 1 0.007 1 0.007 0 0.007
3389 A3389T|(ORF1ab_polyprotein:A3124T(N1042Y))|(ORF1a_polyprotein:A3124T(N1042Y)) 1 0.007 1 0.007 0 0.007
3390 A3390C|(ORF1ab_polyprotein:A3125C(N1042T))|(ORF1a_polyprotein:A3125C(N1042T)) 1 0.007 1 0.007 0 0.007
3398 A3398C|(ORF1ab_polyprotein:A3133C(I1045L))|(ORF1a_polyprotein:A3133C(I1045L)) 2 0.014 1 0.014 0 0.014
3398 A3398C|(ORF1ab_polyprotein:ATT3133-3135CTG(I1045L))|(ORF1a_polyprotein:ATT3133-3135CTG(I1045L)) 1 0.007 1 0.007 0 0.007
3400 T3400G|(ORF1ab_polyprotein:ATT3133-3135CTG(I1045L))|(ORF1a_polyprotein:ATT3133-3135CTG(I1045L)) 1 0.007 1 0.007 0 0.007
3405 A3405T|(ORF1ab_polyprotein:A3140T(E1047V))|(ORF1a_polyprotein:A3140T(E1047V)) 1 0.007 1 0.007 0 0.007
3406 A3406C|(ORF1ab_polyprotein:A3141C(E1047D))|(ORF1a_polyprotein:A3141C(E1047D)) 1 0.007 1 0.007 0 0.007
3406 A3406G|(ORF1ab_polyprotein:A3141G(E1047E))|(ORF1a_polyprotein:A3141G(E1047E)) 1 0.007 1 0.007 0 0.007
3406 A3406T|(ORF1ab_polyprotein:A3141T(E1047D))|(ORF1a_polyprotein:A3141T(E1047D)) 1 0.007 1 0.007 0 0.007
3407 G3407T|(ORF1ab_polyprotein:GAA3142-3144TTA(E1048L))|(ORF1a_polyprotein:GAA3142-3144TTA(E1048L)) 1 0.007 1 0.007 0 0.007
3408 A3408T|(ORF1ab_polyprotein:GAA3142-3144TTA(E1048L))|(ORF1a_polyprotein:GAA3142-3144TTA(E1048L)) 1 0.007 1 0.007 0 0.007
3409 A3409G|(ORF1ab_polyprotein:A3144G(E1048E))|(ORF1a_polyprotein:A3144G(E1048E)) 1 0.007 1 0.007 0 0.007
3410 G3410C|(ORF1ab_polyprotein:G3145C(A1049P))|(ORF1a_polyprotein:G3145C(A1049P)) 1 0.007 1 0.007 0 0.007
3413 A3413C|(ORF1ab_polyprotein:A3148C(K1050Q))|(ORF1a_polyprotein:A3148C(K1050Q)) 1 0.007 1 0.007 0 0.007
3413 A3413C|(ORF1ab_polyprotein:AAA3148-3150CAC(K1050H))|(ORF1a_polyprotein:AAA3148-3150CAC(K1050H)) 1 0.007 1 0.007 0 0.007
3414 A3414C|(ORF1ab_polyprotein:AAA3148-3150ACC(K1050T))|(ORF1a_polyprotein:AAA3148-3150ACC(K1050T)) 1 0.007 1 0.007 0 0.007
3415 A3415C|(ORF1ab_polyprotein:A3150C(K1050N))|(ORF1a_polyprotein:A3150C(K1050N)) 1 0.007 1 0.007 0 0.007
3415 A3415C|(ORF1ab_polyprotein:AAA3148-3150ACC(K1050T))|(ORF1a_polyprotein:AAA3148-3150ACC(K1050T)) 1 0.007 1 0.007 0 0.007
3415 A3415C|(ORF1ab_polyprotein:AAA3148-3150CAC(K1050H))|(ORF1a_polyprotein:AAA3148-3150CAC(K1050H)) 1 0.007 1 0.007 0 0.007
3416 A3416C|(ORF1ab_polyprotein:A3151C(K1051Q))|(ORF1a_polyprotein:A3151C(K1051Q)) 1 0.007 1 0.007 0 0.007
3416 A3416T|(ORF1ab_polyprotein:A3151T(K1051*))|(ORF1a_polyprotein:A3151T(K1051*)) 1 0.007 1 0.007 0 0.007
3416 A3416T|(ORF1ab_polyprotein:AAG3151-3153TTT(K1051F))|(ORF1a_polyprotein:AAG3151-3153TTT(K1051F)) 1 0.007 1 0.007 0 0.007
3417 A3417C|(ORF1ab_polyprotein:A3152C(K1051T))|(ORF1a_polyprotein:A3152C(K1051T)) 1 0.007 1 0.007 0 0.007
3417 A3417T|(ORF1ab_polyprotein:AAG3151-3153TTT(K1051F))|(ORF1a_polyprotein:AAG3151-3153TTT(K1051F)) 1 0.007 1 0.007 0 0.007
3418 G3418T|(ORF1ab_polyprotein:AAG3151-3153TTT(K1051F))|(ORF1a_polyprotein:AAG3151-3153TTT(K1051F)) 1 0.007 1 0.007 0 0.007
3420 T3420C|(ORF1ab_polyprotein:T3155C(V1052A))|(ORF1a_polyprotein:T3155C(V1052A)) 1 0.007 1 0.007 0 0.007
3421 A3421G|(ORF1ab_polyprotein:A3156G(V1052V))|(ORF1a_polyprotein:A3156G(V1052V)) 1 0.007 1 0.007 0 0.007
3421 A3421T|(ORF1ab_polyprotein:A3156T(V1052V))|(ORF1a_polyprotein:A3156T(V1052V)) 1 0.007 1 0.007 0 0.007
3422 A3422T|(ORF1ab_polyprotein:A3157T(K1053*))|(ORF1a_polyprotein:A3157T(K1053*)) 2 0.014 1 0.014 0 0.014
3422 A3422T|(ORF1ab_polyprotein:AAA3157-3159TAT(K1053Y))|(ORF1a_polyprotein:AAA3157-3159TAT(K1053Y)) 1 0.007 1 0.007 0 0.007
3424 A3424T|(ORF1ab_polyprotein:A3159T(K1053N))|(ORF1a_polyprotein:A3159T(K1053N)) 1 0.007 1 0.007 0 0.007
3424 A3424T|(ORF1ab_polyprotein:AAA3157-3159TAT(K1053Y))|(ORF1a_polyprotein:AAA3157-3159TAT(K1053Y)) 1 0.007 1 0.007 0 0.007
3426 C3426G|(ORF1ab_polyprotein:C3161G(P1054R))|(ORF1a_polyprotein:C3161G(P1054R)) 1 0.007 1 0.007 0 0.007
ubiq 3431 G3431T|(ORF1ab_polyprotein:G3166T(V1056L))|(ORF1a_polyprotein:G3166T(V1056L)) 136 0.951 6 0.857 248 0.996 95 1.000 4 0.951 2.8529999999999998 3.804
3431 G3431T|(ORF1ab_polyprotein:GTG3166-3168TNG(V1056?))|(ORF1a_polyprotein:GTG3166-3168TNG(V1056?)) 1 0.007 1 0.007 0 0.007
3432 T3432G|(ORF1ab_polyprotein:T3167G(V1056G))|(ORF1a_polyprotein:T3167G(V1056G)) 1 0.007 1 0.007 0 0.007
3433 G3433T|(ORF1ab_polyprotein:G3168T(V1056V))|(ORF1a_polyprotein:G3168T(V1056V)) 1 0.007 1 0.007 0 0.007
3437 G3437C|(ORF1ab_polyprotein:G3172C(V1058L))|(ORF1a_polyprotein:G3172C(V1058L)) 1 0.007 1 0.007 0 0.007
3440 A3440T|(ORF1ab_polyprotein:A3175T(N1059Y))|(ORF1a_polyprotein:A3175T(N1059Y)) 2 0.014 1 0.014 0 0.014
3445 A3445C|(ORF1ab_polyprotein:A3180C(A1060A))|(ORF1a_polyprotein:A3180C(A1060A)) 1 0.007 1 0.007 0 0.007
3446 G3446T|(ORF1ab_polyprotein:G3181T(A1061S))|(ORF1a_polyprotein:G3181T(A1061S)) 1 0.007 1 0.007 0 0.007
3448 C3448A|(ORF1ab_polyprotein:C3183A(A1061A))|(ORF1a_polyprotein:C3183A(A1061A)) 1 0.007 1 0.007 0 0.007
3449 A3449C|(ORF1ab_polyprotein:A3184C(N1062H))|(ORF1a_polyprotein:A3184C(N1062H)) 1 0.007 1 0.007 0 0.007
3457 C3457G|(ORF1ab_polyprotein:C3192G(Y1064*))|(ORF1a_polyprotein:C3192G(Y1064*)) 1 0.007 1 0.007 0 0.007
3461 A3461C|(ORF1ab_polyprotein:A3196C(K1066Q))|(ORF1a_polyprotein:A3196C(K1066Q)) 1 0.007 1 0.007 0 0.007
3462 A3462T|(ORF1ab_polyprotein:A3197T(K1066I))|(ORF1a_polyprotein:A3197T(K1066I)) 2 0.014 1 0.014 0 0.014
3465 A3465T|(ORF1ab_polyprotein:A3200T(H1067L))|(ORF1a_polyprotein:A3200T(H1067L)) 2 0.014 1 0.014 0 0.014
3466 T3466G|(ORF1ab_polyprotein:T3201G(H1067Q))|(ORF1a_polyprotein:T3201G(H1067Q)) 1 0.007 1 0.007 0 0.007
3471 G3471T|(ORF1ab_polyprotein:G3206T(G1069V))|(ORF1a_polyprotein:G3206T(G1069V)) 1 0.007 1 0.007 0 0.007
3478 T3478G|(ORF1ab_polyprotein:T3213G(V1071V))|(ORF1a_polyprotein:T3213G(V1071V)) 1 0.007 1 0.007 0 0.007
3482 G3482T|(ORF1ab_polyprotein:GGA3217-3219TTA(G1073L))|(ORF1a_polyprotein:GGA3217-3219TTA(G1073L)) 1 0.007 1 0.007 0 0.007
3483 G3483T|(ORF1ab_polyprotein:GGA3217-3219TTA(G1073L))|(ORF1a_polyprotein:GGA3217-3219TTA(G1073L)) 1 0.007 1 0.007 0 0.007
3485 G3485T|(ORF1ab_polyprotein:G3220T(A1074S))|(ORF1a_polyprotein:G3220T(A1074S)) 2 0.014 1 0.014 0 0.014
3487 C3487A|(ORF1ab_polyprotein:C3222A(A1074A))|(ORF1a_polyprotein:C3222A(A1074A)) 1 0.007 1 0.007 0 0.007
3490 A3490T|(ORF1ab_polyprotein:A3225T(L1075F))|(ORF1a_polyprotein:A3225T(L1075F)) 1 0.007 1 0.007 0 0.007
3491 A3491G|(ORF1ab_polyprotein:A3226G(N1076D))|(ORF1a_polyprotein:A3226G(N1076D)) 1 0.007 1 0.007 0 0.007
3495 A3495T|(ORF1ab_polyprotein:A3230T(K1077M))|(ORF1a_polyprotein:A3230T(K1077M)) 1 0.007 1 0.007 0 0.007
3498 C3498A|(ORF1ab_polyprotein:C3233A(A1078D))|(ORF1a_polyprotein:C3233A(A1078D)) 1 0.007 1 0.007 0 0.007
3499 T3499C|(ORF1ab_polyprotein:T3234C(A1078A))|(ORF1a_polyprotein:T3234C(A1078A)) 1 0.007 1 0.007 0 0.007
3508 T3508G|(ORF1ab_polyprotein:T3243G(N1081K))|(ORF1a_polyprotein:T3243G(N1081K)) 1 0.007 1 0.007 0 0.007
3509 3509-insertG|(ORF1ab_polyprotein:3244insertG(1082fs))|(ORF1a_polyprotein:3244insertG(1082fs)) 1 0.007 1 0.007 0 0.007
3509 G3509T|(ORF1ab_polyprotein:G3244T(A1082S))|(ORF1a_polyprotein:G3244T(A1082S)) 1 0.007 1 0.007 0 0.007
3510 C3510A|(ORF1ab_polyprotein:C3245A(A1082D))|(ORF1a_polyprotein:C3245A(A1082D)) 2 0.014 1 0.014 0 0.014
3511 C3511A|(ORF1ab_polyprotein:C3246A(A1082A))|(ORF1a_polyprotein:C3246A(A1082A)) 1 0.006 1 0.006 0 0.006
3516 A3516C|(ORF1ab_polyprotein:A3251C(Q1084P))|(ORF1a_polyprotein:A3251C(Q1084P)) 1 0.006 1 0.006 0 0.006
3516 A3516T|(ORF1ab_polyprotein:A3251T(Q1084L))|(ORF1a_polyprotein:A3251T(Q1084L)) 1 0.006 1 0.006 0 0.006
3519 T3519G|(ORF1ab_polyprotein:T3254G(V1085G))|(ORF1a_polyprotein:T3254G(V1085G)) 1 0.006 1 0.006 0 0.006
3526 T3526G|(ORF1ab_polyprotein:T3261G(S1087S))|(ORF1a_polyprotein:T3261G(S1087S)) 1 0.006 1 0.006 0 0.006
3527 G3527T|(ORF1ab_polyprotein:G3262T(D1088Y))|(ORF1a_polyprotein:G3262T(D1088Y)) 1 0.006 1 0.006 0 0.006
3528 A3528C|(ORF1ab_polyprotein:A3263C(D1088A))|(ORF1a_polyprotein:A3263C(D1088A)) 1 0.006 1 0.006 0 0.006
3528 A3528T|(ORF1ab_polyprotein:A3263T(D1088V))|(ORF1a_polyprotein:A3263T(D1088V)) 1 0.006 1 0.006 0 0.006
3534 A3534T|(ORF1ab_polyprotein:A3269T(Y1090F))|(ORF1a_polyprotein:A3269T(Y1090F)) 3 0.017 1 0.017 0 0.017
3539 G3539T|(ORF1ab_polyprotein:G3274T(A1092S))|(ORF1a_polyprotein:G3274T(A1092S)) 1 0.006 1 0.006 0 0.006
ubiq 3565 T3565C|(ORF1ab_polyprotein:T3300C(G1100G))|(ORF1a_polyprotein:T3300C(G1100G)) 116498 0.996 28421 0.999 30004 0.999 27800 0.731 19097 0.999 9915 0.999 6 0.996 4.727 5.723000000000001
ubiq 4184 G4184A|(ORF1ab_polyprotein:G3919A(G1307S))|(ORF1a_polyprotein:G3919A(G1307S)) 2 1.000 342368 0.996 50871 0.998 21506 0.998 29935 0.998 59140 0.998 6 0.996 4.992 5.9879999999999995
ubiq 4321 C4321T|(ORF1ab_polyprotein:C4056T(A1352A))|(ORF1a_polyprotein:C4056T(A1352A)) 2 1.000 345267 0.991 50694 0.996 21473 0.997 29875 0.997 58284 0.995 6 0.991 4.985 5.976
ubiq 4999 C4999T|(ORF1ab_polyprotein:C4734T(N1578N))|(ORF1a_polyprotein:C4734T(N1578N)) 5 1.000 404216 0.995 1 1.000 50077 0.498 65388 0.718 73786 0.643 107120 0.558 61919 0.395 8 0.995 4.812 5.807
5180 G5180A|(ORF1ab_polyprotein:G4915A(D1639N))|(ORF1a_polyprotein:G4915A(D1639N)) 13503 0.605 1 0.000 1 0.000 2 0.000 4 0.605 0.0 0.605
5720 G5720T|(ORF1ab_polyprotein:G5455T(G1819C))|(ORF1a_polyprotein:G5455T(G1819C)) 1 0.042 6 0.000 9 0.000 8 0.000 5 0.000 3 0.000 32 0.000 7 0.042 0.0 0.042
5730 C5730A|(ORF1ab_polyprotein:C5465A(T1822N))|(ORF1a_polyprotein:C5465A(T1822N)) 1 0.053 17 0.000 15 0.000 12 0.000 9 0.000 7 0.000 42 0.001 7 0.053 0.001 0.054
5732 T5732A|(ORF1ab_polyprotein:T5467A(C1823S))|(ORF1a_polyprotein:T5467A(C1823S)) 1 0.053 29 0.000 19 0.000 14 0.000 9 0.000 8 0.000 30 0.000 7 0.053 0.0 0.053
5878 RATG13 C5878T|(ORF1ab_polyprotein:C5613T(N1871N))|(ORF1a_polyprotein:C5613T(N1871N)) 1 0.500 5 0.000 7 0.000 5 0.000 1 0.000 3 0.000 6 0.000 7 0.5 0.0 0.5
5880 G5880A|(ORF1ab_polyprotein:G5615A(S1872N))|(ORF1a_polyprotein:G5615A(S1872N)) 1 0.500 5 0.000 1 0.000 1 0.000 11 0.000 5 0.5 0.0 0.5
5883 A5883T|(ORF1ab_polyprotein:A5618T(Y1873F))|(ORF1a_polyprotein:A5618T(Y1873F)) 1 0.500 28 0.000 15 0.000 18 0.000 12 0.000 8 0.000 32 0.000 7 0.5 0.0 0.5
5888 A5888C|(ORF1ab_polyprotein:A5623C(T1875P))|(ORF1a_polyprotein:A5623C(T1875P)) 1 0.250 99 0.001 139 0.002 77 0.002 44 0.001 42 0.001 58 0.001 7 0.25 0.008 0.258
5889 C5889G|(ORF1ab_polyprotein:ACA5623-5625AGC(T1875S))|(ORF1a_polyprotein:ACA5623-5625AGC(T1875S)) 1 0.250 1 0.25 0 0.25
5889 C5889T|(ORF1ab_polyprotein:C5624T(T1875I))|(ORF1a_polyprotein:C5624T(T1875I)) 1 0.250 5 0.000 1 0.000 2 0.000 1 0.000 5 0.25 0.0 0.25
5890 A5890C|(ORF1ab_polyprotein:ACA5623-5625AGC(T1875S))|(ORF1a_polyprotein:ACA5623-5625AGC(T1875S)) 1 0.143 1 0.143 0 0.143
5891 A5891T|(ORF1ab_polyprotein:A5626T(T1876S))|(ORF1a_polyprotein:A5626T(T1876S)) 1 0.048 6 0.000 8 0.000 10 0.000 2 0.000 3 0.000 20 0.000 7 0.048 0.0 0.048
5904 T5904A|(ORF1ab_polyprotein:T5639A(V1880D))|(ORF1a_polyprotein:T5639A(V1880D)) 1 0.011 9 0.000 16 0.000 8 0.000 4 0.000 9 0.000 3 0.000 7 0.011 0.0 0.011
5908 T5908A|(ORF1ab_polyprotein:T5643A(T1881T))|(ORF1a_polyprotein:T5643A(T1881T)) 1 0.011 13 0.000 30 0.000 12 0.000 10 0.000 14 0.000 13 0.000 7 0.011 0.0 0.011
5910 A5910G|(ORF1ab_polyprotein:A5645G(Y1882C))|(ORF1a_polyprotein:A5645G(Y1882C)) 1 0.011 2 0.000 2 0.000 6 0.000 1 0.000 1 0.000 1 0.000 7 0.011 0.0 0.011
5911 T5911A|(ORF1ab_polyprotein:T5646A(Y1882*))|(ORF1a_polyprotein:T5646A(Y1882*)) 2 0.022 6 0.000 13 0.000 6 0.000 5 0.000 4 0.000 4 0.000 7 0.022 0.0 0.022
5918 G5918T|(ORF1ab_polyprotein:G5653T(D1885Y))|(ORF1a_polyprotein:G5653T(D1885Y)) 1 0.011 20 0.000 9 0.000 13 0.000 5 0.000 4 0.000 22 0.000 7 0.011 0.0 0.011
linked 6007 T6007G|(ORF1ab_polyprotein:T5742G(L1914L))|(ORF1a_polyprotein:T5742G(L1914L)) 62 0.000 57 0.000 76 0.000 1 0.000 15 0.000 37 0.000 19 0.000 7 0.0 0.0 0.0
linked 6131 A6131T|(ORF1ab_polyprotein:AAA5866-5868TTA(K1956L))|(ORF1a_polyprotein:AAA5866-5868TTA(K1956L)) 62 0.000 13 0.000 10 0.000 7 0.000 33 0.000 5 0.0 0.0 0.0
linked 6132 A6132T|(ORF1ab_polyprotein:AAA5866-5868TTA(K1956L))|(ORF1a_polyprotein:AAA5866-5868TTA(K1956L)) 62 0.000 13 0.000 10 0.000 7 0.000 33 0.000 5 0.0 0.0 0.0
linkedubiq 6183 A6183G|(ORF1ab_polyprotein:A5918G(K1973R))|(ORF1a_polyprotein:A5918G(K1973R)) 2 0.667 301172 0.996 145233 0.999 102054 0.999 1 1.000 35761 0.999 85618 0.999 194144 0.998 8 0.996 6.661 7.657
linked 6206 A6206T|(ORF1ab_polyprotein:A5941T(K1981*))|(ORF1a_polyprotein:A5941T(K1981*)) 800 0.003 128 0.001 90 0.001 24 0.001 85 0.001 341 0.002 6 0.003 0.006 0.009000000000000001
linked 6215 A6215T|(ORF1ab_polyprotein:AAA5950-5952TAT(K1984Y))|(ORF1a_polyprotein:AAA5950-5952TAT(K1984Y)) 47 0.000 6 0.000 1 0.000 2 0.000 3 0.000 13 0.000 6 0.0 0.0 0.0
linked 6217 A6217T|(ORF1ab_polyprotein:AAA5950-5952TAT(K1984Y))|(ORF1a_polyprotein:AAA5950-5952TAT(K1984Y)) 47 0.000 6 0.000 1 0.000 2 0.000 3 0.000 13 0.000 6 0.0 0.0 0.0
linked 6255 C6255T|(ORF1ab_polyprotein:C5990T(A1997V))|(ORF1a_polyprotein:C5990T(A1997V)) 1 0.333 293169 0.777 173079 1.000 103235 0.877 1 1.000 49548 0.599 101453 0.658 172894 0.655 8 0.777 5.122 5.899
6510 A6510G|(ORF1ab_polyprotein:A6245G(N2082S))|(ORF1a_polyprotein:A6245G(N2082S)) 83765 0.991 6 0.000 1 0.000 2 0.000 3 0.000 8 0.000 6 0.991 0.0 0.991
6858 T6858A|(ORF1ab_polyprotein:T6593A(I2198K))|(ORF1a_polyprotein:T6593A(I2198K)) 1 0.016 23 0.000 13 0.000 7 0.000 7 0.000 52 0.000 127 0.001 7 0.016 0.001 0.017
6879 G6879T|(ORF1ab_polyprotein:G6614T(S2205I))|(ORF1a_polyprotein:G6614T(S2205I)) 1 0.015 8 0.000 6 0.000 6 0.000 6 0.000 17 0.000 93 0.001 7 0.015 0.001 0.016
6880 T6880A|(ORF1ab_polyprotein:T6615A(S2205R))|(ORF1a_polyprotein:T6615A(S2205R)) 1 0.015 8 0.000 4 0.000 5 0.000 4 0.000 30 0.000 38 0.000 7 0.015 0.0 0.015
6882 T6882A|(ORF1ab_polyprotein:T6617A(V2206D))|(ORF1a_polyprotein:T6617A(V2206D)) 2 0.031 13 0.000 10 0.000 4 0.000 6 0.000 34 0.000 66 0.000 7 0.031 0.0 0.031
6889 A6889C|(ORF1ab_polyprotein:A6624C(K2208N))|(ORF1a_polyprotein:A6624C(K2208N)) 1 0.015 6 0.000 6 0.000 1 0.000 2 0.000 17 0.000 8 0.000 7 0.015 0.0 0.015
6890 T6890A|(ORF1ab_polyprotein:TTT6625-6627ATA(F2209I))|(ORF1a_polyprotein:TTT6625-6627ATA(F2209I)) 1 0.015 2 0.000 2 0.000 2 0.000 9 0.000 5 0.015 0.0 0.015
6892 T6892A|(ORF1ab_polyprotein:TTT6625-6627ATA(F2209I))|(ORF1a_polyprotein:TTT6625-6627ATA(F2209I)) 1 0.015 2 0.000 2 0.000 2 0.000 9 0.000 5 0.015 0.0 0.015
6895 T6895A|(ORF1ab_polyprotein:T6630A(C2210*))|(ORF1a_polyprotein:T6630A(C2210*)) 1 0.015 11 0.000 10 0.000 6 0.000 2 0.000 20 0.000 49 0.000 7 0.015 0.0 0.015
6901 G6901T|(ORF1ab_polyprotein:G6636T(E2212D))|(ORF1a_polyprotein:G6636T(E2212D)) 1 0.015 14 0.000 3 0.000 5 0.000 3 0.000 27 0.000 129 0.001 7 0.015 0.001 0.016
6911 A6911T|(ORF1ab_polyprotein:A6646T(N2216Y))|(ORF1a_polyprotein:A6646T(N2216Y)) 1 0.015 10 0.000 8 0.000 3 0.000 5 0.000 35 0.000 23 0.000 7 0.015 0.0 0.015
6933 T6933A|(ORF1ab_polyprotein:T6668A(F2223Y))|(ORF1a_polyprotein:T6668A(F2223Y)) 1 0.015 19 0.000 7 0.000 12 0.001 5 0.000 46 0.000 91 0.001 7 0.015 0.002 0.017
6935 T6935A|(ORF1ab_polyprotein:T6670A(S2224T))|(ORF1a_polyprotein:T6670A(S2224T)) 1 0.015 15 0.000 6 0.000 8 0.000 8 0.000 31 0.000 56 0.000 7 0.015 0.0 0.015
6937 T6937C|(ORF1ab_polyprotein:T6672C(S2224S))|(ORF1a_polyprotein:T6672C(S2224S)) 1 0.015 4 0.000 3 0.000 3 0.000 2 0.000 20 0.000 5 0.000 7 0.015 0.0 0.015
6948 A6948T|(ORF1ab_polyprotein:A6683T(N2228I))|(ORF1a_polyprotein:A6683T(N2228I)) 1 0.015 16 0.000 16 0.001 5 0.000 5 0.000 33 0.000 27 0.000 7 0.015 0.001 0.016
6950 A6950G|(ORF1ab_polyprotein:A6685G(I2229V))|(ORF1a_polyprotein:A6685G(I2229V)) 1 0.015 22 0.000 14 0.001 5 0.000 11 0.001 22 0.000 29 0.000 7 0.015 0.002 0.017
6956 A6956C|(ORF1ab_polyprotein:ATT6691-6693CGT(I2231R))|(ORF1a_polyprotein:ATT6691-6693CGT(I2231R)) 1 0.015 4 0.000 1 0.000 1 0.000 5 0.000 2 0.000 6 0.015 0.0 0.015
6957 T6957G|(ORF1ab_polyprotein:ATT6691-6693CGT(I2231R))|(ORF1a_polyprotein:ATT6691-6693CGT(I2231R)) 1 0.015 4 0.000 1 0.000 1 0.000 5 0.000 2 0.000 6 0.015 0.0 0.015
6961 G6961C|(ORF1ab_polyprotein:G6696C(W2232C))|(ORF1a_polyprotein:G6696C(W2232C)) 1 0.015 2 0.000 3 0.000 3 0.015 0.0 0.015
6975 G6975C|(ORF1ab_polyprotein:AGT6709-6711ACA(S2237T))|(ORF1a_polyprotein:AGT6709-6711ACA(S2237T)) 1 0.015 1 0.000 1 0.000 4 0.000 4 0.015 0.0 0.015
6976 T6976A|(ORF1ab_polyprotein:AGT6709-6711ACA(S2237T))|(ORF1a_polyprotein:AGT6709-6711ACA(S2237T)) 1 0.015 1 0.000 1 0.000 4 0.000 4 0.015 0.0 0.015
6977 G6977A|(ORF1ab_polyprotein:GTT6712-6714ATA(V2238I))|(ORF1a_polyprotein:GTT6712-6714ATA(V2238I)) 1 0.015 1 0.015 0 0.015
6979 T6979A|(ORF1ab_polyprotein:GTT6712-6714ATA(V2238I))|(ORF1a_polyprotein:GTT6712-6714ATA(V2238I)) 1 0.015 1 0.015 0 0.015
6993 T6993G|(ORF1ab_polyprotein:T6728G(L2243*))|(ORF1a_polyprotein:T6728G(L2243*)) 1 0.015 20 0.000 15 0.001 6 0.000 8 0.000 61 0.001 45 0.000 7 0.015 0.002 0.017
6995 A6995G|(ORF1ab_polyprotein:A6730G(I2244V))|(ORF1a_polyprotein:A6730G(I2244V)) 1 0.015 19 0.000 13 0.000 9 0.000 2 0.000 51 0.000 50 0.000 7 0.015 0.0 0.015
7040 A7040T|(ORF1ab_polyprotein:ATG6775-6777TGG(M2259W))|(ORF1a_polyprotein:ATG6775-6777TGG(M2259W)) 1 0.015 1 0.000 2 0.015 0.0 0.015
7041 T7041G|(ORF1ab_polyprotein:ATG6775-6777TGG(M2259W))|(ORF1a_polyprotein:ATG6775-6777TGG(M2259W)) 1 0.015 1 0.000 2 0.015 0.0 0.015
7048 T7048G|(ORF1ab_polyprotein:T6783G(S2261S))|(ORF1a_polyprotein:T6783G(S2261S)) 1 0.015 22 0.000 19 0.001 7 0.000 6 0.000 41 0.000 52 0.000 7 0.015 0.001 0.016
7103 A7103C|(ORF1ab_polyprotein:ACC6838-6840CAC(T2280H))|(ORF1a_polyprotein:ACC6838-6840CAC(T2280H)) 1 0.016 1 0.000 4 0.000 1 0.000 3 0.000 3 0.000 13 0.000 7 0.016 0.0 0.016
7104 C7104A|(ORF1ab_polyprotein:ACC6838-6840CAC(T2280H))|(ORF1a_polyprotein:ACC6838-6840CAC(T2280H)) 1 0.016 1 0.000 4 0.000 1 0.000 3 0.000 3 0.000 13 0.000 7 0.016 0.0 0.016
ubiq 7113 C7113T|(ORF1ab_polyprotein:C6848T(T2283I))|(ORF1a_polyprotein:C6848T(T2283I)) 2 1.000 62 1.000 52235 0.997 2 0.000 22346 0.997 12517 0.734 67396 0.563 141825 0.996 8 1.0 5.287 6.287
7117 T7117G|(ORF1ab_polyprotein:T6852G(G2284G))|(ORF1a_polyprotein:T6852G(G2284G)) 1 0.016 17 0.000 43 0.002 7 0.000 3 0.000 56 0.000 31 0.000 7 0.016 0.002 0.018000000000000002
7121 A7121T|(ORF1ab_polyprotein:A6856T(I2286L))|(ORF1a_polyprotein:A6856T(I2286L)) 1 0.016 16 0.000 9 0.000 9 0.000 5 0.000 29 0.000 47 0.000 7 0.016 0.0 0.016
7757 A7757G|(ORF1ab_polyprotein:A7492G(N2498D))|(ORF1a_polyprotein:A7492G(N2498D)) 1 1.000 1 0.000 3 0.000 3 1.0 0.0 1.0
7760 GG7760-7761del|(ORF1ab_polyprotein:GGTTCC7495-7500TTCdel(GS2499-2500Fdel))|(ORF1a_polyprotein:GGTTCC7495-7500TTCdel(GS2499-2500Fdel)) 1 1.000 1 1.0 0 1.0
7764 C7764-7764del|(ORF1ab_polyprotein:GGTTCC7495-7500TTCdel(GS2499-2500Fdel))|(ORF1a_polyprotein:GGTTCC7495-7500TTCdel(GS2499-2500Fdel)) 1 1.000 1 1.0 0 1.0
7767 T7767A|(ORF1ab_polyprotein:T7502A(I2501N))|(ORF1a_polyprotein:T7502A(I2501N)) 1 0.143 5 0.000 1 0.000 2 0.000 4 0.143 0.0 0.143
7769 7769-insertGA|(ORF1ab_polyprotein:7504insertGA(2502fs))|(ORF1a_polyprotein:7504insertGA(2502fs)) 1 0.020 1 0.02 0 0.02
7777 C7777A|(ORF1ab_polyprotein:C7512A(Y2504*))|(ORF1a_polyprotein:C7512A(Y2504*)) 1 0.019 10 0.001 2 0.000 2 0.000 5 0.001 5 0.019 0.002 0.020999999999999998
7781 G7781T|(ORF1ab_polyprotein:GAT7516-7518TTT(D2506F))|(ORF1a_polyprotein:GAT7516-7518TTT(D2506F)) 1 0.018 1 0.018 0 0.018
7782 A7782T|(ORF1ab_polyprotein:GAT7516-7518TTT(D2506F))|(ORF1a_polyprotein:GAT7516-7518TTT(D2506F)) 1 0.018 1 0.018 0 0.018
7787 G7787T|(ORF1ab_polyprotein:GCT7522-7524TAT(A2508Y))|(ORF1a_polyprotein:GCT7522-7524TAT(A2508Y)) 1 0.017 1 0.000 2 0.017 0.0 0.017
7788 C7788A|(ORF1ab_polyprotein:GCT7522-7524TAT(A2508Y))|(ORF1a_polyprotein:GCT7522-7524TAT(A2508Y)) 1 0.017 1 0.000 2 0.017 0.0 0.017
7790 G7790T|(ORF1ab_polyprotein:G7525T(G2509C))|(ORF1a_polyprotein:G7525T(G2509C)) 1 0.016 3 0.000 3 0.000 3 0.000 2 0.000 5 0.016 0.0 0.016
7793 C7793G|(ORF1ab_polyprotein:C7528G(Q2510E))|(ORF1a_polyprotein:C7528G(Q2510E)) 2 0.033 2 0.000 1 0.000 3 0.033 0.0 0.033
7795 A7795T|(ORF1ab_polyprotein:A7530T(Q2510H))|(ORF1a_polyprotein:A7530T(Q2510H)) 1 0.016 5 0.000 1 0.000 4 0.001 4 0.001 5 0.016 0.002 0.018000000000000002
7797 A7797T|(ORF1ab_polyprotein:A7532T(K2511M))|(ORF1a_polyprotein:A7532T(K2511M)) 1 0.016 2 0.000 1 0.000 1 0.000 4 0.016 0.0 0.016
linkedubiq 7842 A7842G|(ORF1ab_polyprotein:A7577G(N2526S))|(ORF1a_polyprotein:A7577G(N2526S)) 1 1.000 162190 0.995 1 1.000 93752 0.998 29833 0.998 5 0.995 3.996 4.991
7941 T7941-7941del|(ORF1ab_polyprotein:7676-7676del(2559fs))|(ORF1a_polyprotein:7676-7676del(2559fs)) 164773 0.994 7 0.000 2 0.994 0.0 0.994
8148 A8148C|(ORF1ab_polyprotein:AAT7882-7884ACA(N2628T))|(ORF1a_polyprotein:AAT7882-7884ACA(N2628T)) 51 0.000 1 0.030 3 0.000 1 0.000 3 0.000 5 0.03 0.0 0.03
8149 T8149A|(ORF1ab_polyprotein:AAT7882-7884ACA(N2628T))|(ORF1a_polyprotein:AAT7882-7884ACA(N2628T)) 51 0.000 1 0.030 3 0.000 1 0.000 3 0.000 5 0.03 0.0 0.03
ubiq 8293 C8293T|(ORF1ab_polyprotein:C8028T(T2676T))|(ORF1a_polyprotein:C8028T(T2676T)) 2204239 0.992 1 1.000 213885 0.996 103775 0.996 54430 0.995 98903 0.996 6 1.0 4.975 5.975
ubiq 8393 G8393A|(ORF1ab_polyprotein:G8128A(A2710T))|(ORF1a_polyprotein:G8128A(A2710T)) 2173730 0.993 1 1.000 212025 0.997 102820 0.997 54005 0.996 98052 0.997 6 1.0 4.98 5.98
ubiq 10029 C10029T|(ORF1ab_polyprotein:C9764T(T3255I))|(ORF1a_polyprotein:C9764T(T3255I)) 4582 0.993 5427 0.998 1714 0.997 1321 0.998 1954 0.998 4304 0.998 6 0.993 4.989 5.982
ubiq 10198 C10198T|(ORF1ab_polyprotein:C9933T(D3311D))|(ORF1a_polyprotein:C9933T(D3311D)) 4590 0.996 5434 0.998 1718 0.998 1329 1.000 1961 0.998 4324 0.999 6 0.996 4.993 5.989000000000001
linkedubiq 10447 RATG13 G10447A|(ORF1ab_polyprotein:G10182A(R3394R))|(ORF1a_polyprotein:G10182A(R3394R)) 2 1.000 3 1.000 39931 0.999 27297 0.999 4 1.0 2.998 3.998
linkedubiq 10449 C10449A|(ORF1ab_polyprotein:C10184A(P3395H))|(ORF1a_polyprotein:C10184A(P3395H)) 2 1.000 3 1.000 39922 0.998 27285 0.998 4 1.0 2.996 3.996
10471 A10471G|(ORF1ab_polyprotein:A10206G(S3402S))|(ORF1a_polyprotein:A10206G(S3402S)) 1 0.500 4 0.000 3 0.000 3 0.5 0.0 0.5
10517 G10517T|(ORF1ab_polyprotein:G10252T(D3418Y))|(ORF1a_polyprotein:G10252T(D3418Y)) 1 0.333 8 0.000 4 0.000 3 0.333 0.0 0.333
10520 T10520C|(ORF1ab_polyprotein:T10255C(C3419R))|(ORF1a_polyprotein:T10255C(C3419R)) 1 0.333 7 0.000 6 0.000 3 0.333 0.0 0.333
10523 G10523-10523del|(ORF1ab_polyprotein:10258-10258del(3420fs))|(ORF1a_polyprotein:10258-10258del(3420fs)) 1 0.333 1 0.333 0 0.333
10527 C10527A|(ORF1ab_polyprotein:C10262A(S3421Y))|(ORF1a_polyprotein:C10262A(S3421Y)) 1 0.333 11 0.000 13 0.000 3 0.333 0.0 0.333
10548 T10548G|(ORF1ab_polyprotein:T10283G(M3428R))|(ORF1a_polyprotein:T10283G(M3428R)) 1 0.023 1 0.000 4 0.000 3 0.023 0.0 0.023
10747 C10747T|(ORF1ab_polyprotein:C10482T(N3494N))|(ORF1a_polyprotein:C10482T(N3494N)) 69093 0.504 1 0.000 9 0.000 7 0.000 1 0.000 4 0.000 6 0.504 0.0 0.504
10898 T10898A|(ORF1ab_polyprotein:T10633A(L3545M))|(ORF1a_polyprotein:T10633A(L3545M)) 1 0.006 5 0.000 5 0.000 9 0.000 10 0.000 52 0.000 6 0.006 0.0 0.006
10901 G10901T|(ORF1ab_polyprotein:G10636T(G3546C))|(ORF1a_polyprotein:G10636T(G3546C)) 1 0.029 12 0.001 10 0.000 15 0.001 22 0.001 132 0.001 6 0.029 0.004 0.033
10910 T10910A|(ORF1ab_polyprotein:T10645A(L3549I))|(ORF1a_polyprotein:T10645A(L3549I)) 1 0.032 8 0.000 9 0.000 6 0.000 12 0.000 76 0.001 6 0.032 0.001 0.033
10920 A10920T|(ORF1ab_polyprotein:A10655T(D3552V))|(ORF1a_polyprotein:A10655T(D3552V)) 1 0.043 4 0.000 1 0.000 7 0.000 6 0.000 5 0.000 6 0.043 0.0 0.043
10925 T10925A|(ORF1ab_polyprotein:T10660A(F3554I))|(ORF1a_polyprotein:T10660A(F3554I)) 1 0.045 15 0.001 17 0.001 10 0.000 19 0.001 59 0.001 6 0.045 0.004 0.049
10927 T10927A|(ORF1ab_polyprotein:T10662A(F3554L))|(ORF1a_polyprotein:T10662A(F3554L)) 1 0.062 18 0.001 24 0.001 15 0.001 24 0.001 107 0.001 6 0.062 0.005 0.067
10928 AC10928-10929del|(ORF1ab_polyprotein:ACA10663-10665Tdel(T3555del;fs))|(ORF1a_polyprotein:ACA10663-10665Tdel(T3555del;fs)) 1 0.500 1 0.5 0 0.5
10930 A10930T|(ORF1ab_polyprotein:ACA10663-10665Tdel(T3555del;fs))|(ORF1a_polyprotein:ACA10663-10665Tdel(T3555del;fs)) 1 0.500 1 0.5 0 0.5
ubiq 11288 TCTGGTTTT11288-11296del|(ORF1ab_polyprotein:11023-11031del(SGF3675-3677del))|(ORF1a_polyprotein:11023-11031del(SGF3675-3677del)) 1 1.000 6591 0.999 10372 0.999 13336 0.999 17039 0.998 5150 0.999 6 1.0 4.994 5.994
ubiq 11727 G11727A|(ORF1ab_polyprotein:G11462A(R3821K))|(ORF1a_polyprotein:G11462A(R3821K)) 24229 0.994 1919 0.993 2836 0.997 1704 0.998 854 0.998 1121 0.998 1978 0.997 3965 0.997 8 0.993 6.979 7.972
12389 A12389T|(ORF1ab_polyprotein:A12124T(N4042Y))|(ORF1a_polyprotein:A12124T(N4042Y)) 2 0.286 56 0.001 52 0.001 13 0.001 21 0.001 9 0.001 68 0.002 7 0.286 0.007 0.293
12672 C12672T|(ORF1ab_polyprotein:C12407T(A4136V))|(ORF1a_polyprotein:C12407T(A4136V)) 6 0.005 1 0.005 0 0.005
12687 A12687T|(ORF1ab_polyprotein:A12422T(N4141I))|(ORF1a_polyprotein:A12422T(N4141I)) 5 0.005 1 0.000 2 0.005 0.0 0.005
ubiq 12789 C12789T|(ORF1ab_polyprotein:C12524T(T4175I))|(ORF1a_polyprotein:C12524T(T4175I)) 1 1.000 28887 0.996 7085 0.948 4042 0.995 8686 0.997 12832 0.997 6 1.0 4.933 5.933
ubiq 13339 T13339C|(ORF1ab_polyprotein:T13074C(N4358N))|(ORF1a_polyprotein:T13074C(N4358N)) 1411 0.992 46822 0.995 21678 0.360 1 1.000 28591 0.994 15273 0.994 21308 0.995 7 0.992 5.338 6.33
13809 A13809C|(ORF1ab_polyprotein:A13545C(T4515T)) 1 0.023 4 0.000 7 0.000 2 0.000 11 0.000 17 0.000 6 0.023 0.0 0.023
13810 A13810C|(ORF1ab_polyprotein:A13546C(M4516L)) 1 0.023 3 0.000 12 0.000 4 0.000 3 0.000 10 0.000 25 0.000 7 0.023 0.0 0.023
14071 G14071C|(ORF1ab_polyprotein:GAT13807-13809CTT(D4603L)) 1 0.100 2 0.000 2 0.1 0.0 0.1
14072 A14072T|(ORF1ab_polyprotein:GAT13807-13809CTT(D4603L)) 1 0.091 2 0.000 2 0.091 0.0 0.091
14073 T14073-14073del|(ORF1ab_polyprotein:13809-13809del(4603fs)) 2 0.167 2 0.000 2 0.167 0.0 0.167
14073 T14073C|(ORF1ab_polyprotein:T13809C(D4603D)) 1 0.083 1 0.000 9 0.000 1 0.000 2 0.000 8 0.000 25 0.000 7 0.083 0.0 0.083
14073 T14073G|(ORF1ab_polyprotein:T13809G(D4603E)) 3 0.250 5 0.000 3 0.000 3 0.25 0.0 0.25
14083 A14083C|(ORF1ab_polyprotein:A13819C(N4607H)) 1 0.030 1 0.000 3 0.000 3 0.03 0.0 0.03
linkedubiq 14408 Delta C14408T|(ORF1ab_polyprotein:C14144T(P4715L)) 3 1.000 97707 0.997 98449 0.999 69562 0.999 66126 0.999 48616 0.999 76855 0.999 378983 0.999 8 0.997 6.994 7.991
14801 A14801G|(ORF1ab_polyprotein:A14537G(D4846G)) 7112 0.465 3 0.000 1 0.000 4 0.000 2 0.000 5 0.465 0.0 0.465
15480 C15480A|(ORF1ab_polyprotein:C15216A(T5072T)) 48016 0.996 15 0.001 11 0.000 9 0.000 26 0.000 14 0.000 154 0.001 7 0.996 0.002 0.998
15540 RATG13 C15540T|(ORF1ab_polyprotein:C15276T(V5092V)) 48803 0.992 1 0.000 5 0.000 4 0.000 3 0.000 5 0.000 6 0.992 0.0 0.992
ubiq 15714 RATG13 C15714T|(ORF1ab_polyprotein:C15450T(L5150L)) 11357 0.993 14652 0.998 3299 0.995 4891 0.998 4944 0.998 5620 0.998 29563 0.997 7 0.993 5.984 6.977
ubiq 15756 T15756A|(ORF1ab_polyprotein:T15492A(S5164S)) 11433 0.996 14720 0.999 3329 0.997 4907 0.998 5191 0.999 5719 0.999 30237 0.998 7 0.996 5.99 6.986000000000001
16624 C16624-16624del|(ORF1ab_polyprotein:16360-16360del(5454fs)) 2 0.200 1 0.006 3 0.001 3 0.2 0.007 0.20700000000000002
16624 C16624G|(ORF1ab_polyprotein:C16360G(L5454V)) 2 0.200 1 0.2 0 0.2
16625 16625-insertA|(ORF1ab_polyprotein:16361insertA(5454fs)) 1 0.009 1 0.009 0 0.009
16636 G16636T|(ORF1ab_polyprotein:G16372T(A5458S)) 1 0.008 1 0.000 2 0.008 0.0 0.008
16645 A16645C|(ORF1ab_polyprotein:A16381C(T5461P)) 1 0.006 2 0.000 2 0.006 0.0 0.006
16957 G16957A|(ORF1ab_polyprotein:G16693A(V5565M)) 148769 0.351 1 0.000 1 0.000 1 0.000 1 0.000 5 0.351 0.0 0.351
17005 A17005C|(ORF1ab_polyprotein:A16741C(N5581H)) 1 0.009 4 0.000 2 0.009 0.0 0.009
17005 A17005T|(ORF1ab_polyprotein:A16741T(N5581Y)) 1 0.009 1 0.000 1 0.000 3 0.000 3 0.000 5 0.009 0.0 0.009
17027 G17027C|(ORF1ab_polyprotein:G16763C(S5588T)) 1 0.011 1 0.000 1 0.000 3 0.011 0.0 0.011
17030 A17030T|(ORF1ab_polyprotein:A16766T(N5589I)) 1 0.011 1 0.000 2 0.011 0.0 0.011
17034 17034-insertA|(ORF1ab_polyprotein:GTTGCA16768-16773GTATGA(VA5590-5591V*)) 1 0.019 1 0.019 0 0.019
17034 TGC17034-17036del|(ORF1ab_polyprotein:GTTGCA16768-16773GTAdel(VA5590-5591Vdel)) 2 0.074 1 0.074 0 0.074
17036 C17036-17036del|(ORF1ab_polyprotein:GTTGCA16768-16773GTATGA(VA5590-5591V*)) 1 0.037 1 0.037 0 0.037
17050 G17050C|(ORF1ab_polyprotein:G16786C(V5596L)) 1 0.042 1 0.000 6 0.000 3 0.042 0.0 0.042
17133 C17133G|(ORF1ab_polyprotein:C16869G(Y5623*)) 1 0.043 2 0.000 2 0.000 3 0.043 0.0 0.043
17143 C17143G|(ORF1ab_polyprotein:C16879G(R5627G)) 1 0.043 2 0.000 1 0.000 3 0.043 0.0 0.043
17161 T17161A|(ORF1ab_polyprotein:T16897A(C5633S)) 1 0.043 7 0.001 24 0.001 13 0.001 9 0.001 5 0.043 0.004 0.047
17182 G17182-17182del|(ORF1ab_polyprotein:16918-16918del(5640fs)) 1 0.029 1 0.029 0 0.029
17182 G17182T|(ORF1ab_polyprotein:G16918T(A5640S)) 3 0.086 2 0.000 5 0.000 5 0.000 4 0.000 5 0.086 0.0 0.086
17183 17183-insertA|(ORF1ab_polyprotein:16919insertA(5640fs)) 1 0.011 1 0.011 0 0.011
17188 T17188G|(ORF1ab_polyprotein:TGT16924-16926GCT(C5642A)) 1 0.010 1 0.01 0 0.01
17189 G17189C|(ORF1ab_polyprotein:TGT16924-16926GCT(C5642A)) 1 0.010 1 0.01 0 0.01
17197 G17197C|(ORF1ab_polyprotein:G16933C(A5645P)) 1 0.010 1 0.000 2 0.000 1 0.000 4 0.01 0.0 0.01
17198 C17198A|(ORF1ab_polyprotein:C16934A(A5645E)) 1 0.010 1 0.000 6 0.000 5 0.000 4 0.000 5 0.01 0.0 0.01
17205 A17205G|(ORF1ab_polyprotein:A16941G(K5647K)) 1 0.009 1 0.000 2 0.009 0.0 0.009
17210 T17210A|(ORF1ab_polyprotein:T16946A(L5649*)) 1 0.008 1 0.000 1 0.000 3 0.008 0.0 0.008
17211 G17211T|(ORF1ab_polyprotein:G16947T(L5649F)) 1 0.008 1 0.000 2 0.000 3 0.000 3 0.000 5 0.008 0.0 0.008
linked 17410 C17410T|(ORF1ab_polyprotein:C17146T(R5716C)) 203285 0.745 1 1.000 48483 0.997 3868 0.998 39220 0.998 28583 0.998 113518 0.998 7 0.745 5.989 6.734
17430 C17430T|(ORF1ab_polyprotein:C17166T(Y5722Y)) 71241 0.262 2 0.000 3 0.000 1 0.000 2 0.000 5 0.262 0.0 0.262
17556 T17556A|(ORF1ab_polyprotein:T17292A(T5764T)) 1 0.023 12 0.000 35 0.000 6 0.000 13 0.000 15 0.000 35 0.001 7 0.023 0.001 0.024
17558 G17558T|(ORF1ab_polyprotein:G17294T(C5765F)) 1 0.023 11 0.000 29 0.000 6 0.000 13 0.000 19 0.000 55 0.001 7 0.023 0.001 0.024
17560 C17560A|(ORF1ab_polyprotein:CGG17296-17298AGT(R5766S)) 1 0.023 1 0.000 1 0.000 3 0.000 4 0.023 0.0 0.023
17561 G17561T|(ORF1ab_polyprotein:G17297T(R5766L)) 1 0.023 7 0.000 25 0.000 1 0.000 12 0.000 13 0.000 46 0.001 7 0.023 0.001 0.024
17562 G17562T|(ORF1ab_polyprotein:CGG17296-17298AGT(R5766S)) 1 0.023 1 0.000 1 0.000 3 0.000 4 0.023 0.0 0.023
17563 C17563A|(ORF1ab_polyprotein:C17299A(R5767S)) 1 0.024 7 0.000 25 0.000 3 0.000 16 0.000 19 0.000 29 0.001 7 0.024 0.001 0.025
17567 G17567T|(ORF1ab_polyprotein:G17303T(C5768F)) 2 0.053 3 0.000 20 0.000 7 0.000 10 0.000 12 0.000 33 0.001 7 0.053 0.001 0.054
17569 C17569A|(ORF1ab_polyprotein:C17305A(P5769T)) 2 0.056 2 0.000 8 0.000 1 0.000 5 0.000 6 0.000 14 0.000 7 0.056 0.0 0.056
17571 T17571A|(ORF1ab_polyprotein:T17307A(P5769P)) 1 0.030 15 0.000 35 0.000 6 0.000 21 0.000 29 0.000 46 0.001 7 0.03 0.001 0.031
17574 T17574A|(ORF1ab_polyprotein:T17310A(A5770A)) 1 0.032 8 0.000 18 0.000 4 0.000 10 0.000 20 0.000 6 0.032 0.0 0.032
17810 T17810-17810del|(ORF1ab_polyprotein:17546-17546del(5849fs)) 4 0.571 3 0.000 8 0.000 1 0.000 12 0.000 9 0.000 10 0.000 7 0.571 0.0 0.571
17812 T17812A|(ORF1ab_polyprotein:T17548A(L5850M)) 2 0.222 4 0.000 16 0.000 2 0.000 11 0.000 15 0.000 1 0.000 7 0.222 0.0 0.222
17812 T17812G|(ORF1ab_polyprotein:T17548G(L5850V)) 4 0.444 8 0.000 64 0.001 3 0.000 19 0.000 22 0.000 7 0.000 7 0.444 0.001 0.445
17813 T17813A|(ORF1ab_polyprotein:T17549A(L5850*)) 1 0.077 6 0.000 27 0.000 4 0.000 8 0.000 19 0.000 1 0.000 7 0.077 0.0 0.077
17822 C17822A|(ORF1ab_polyprotein:C17558A(P5853Q)) 1 0.045 12 0.000 35 0.000 3 0.000 15 0.000 20 0.000 44 0.001 7 0.045 0.001 0.046
linked 18163 A18163G|(ORF1ab_polyprotein:A17899G(I5967V)) 80982 0.692 3731 0.999 11150 0.999 4605 0.998 22749 0.999 19697 0.999 36486 0.998 7 0.692 5.992 6.684
18181 G18181T|(ORF1ab_polyprotein:G17917T(D5973Y)) 3239 0.047 4 0.001 4 0.000 5 0.000 4 0.000 4 0.000 6 0.047 0.001 0.048
18424 A18424G|(ORF1ab_polyprotein:A18160G(N6054D)) 9532 0.366 1 0.000 3 0.000 3 0.366 0.0 0.366
linked 18492 A18492G|(ORF1ab_polyprotein:A18228G(P6076P)) 16289 0.630 3732 0.999 5877 0.998 4604 0.999 6450 0.998 8511 0.271 3661 0.996 7 0.63 5.261 5.891
18891 G18891A|(ORF1ab_polyprotein:G18627A(E6209E)) 48839 0.995 3 0.000 1 0.000 3 0.000 3 0.000 2 0.000 4 0.000 7 0.995 0.0 0.995
linkedubiq 18894 C18894T|(ORF1ab_polyprotein:C18630T(C6210C)) 1 1.000 48690 0.992 105941 0.998 57842 0.996 157617 0.997 48763 0.665 98698 0.997 182541 0.996 8 0.992 6.649 7.641
19481 G19481T|(ORF1ab_polyprotein:G19217T(G6406V)) 1 0.013 38 0.000 36 0.000 89 0.000 19 0.000 39 0.000 135 0.001 7 0.013 0.001 0.013999999999999999
19484 C19484A|(ORF1ab_polyprotein:C19220A(A6407D)) 1 0.013 49 0.000 61 0.000 87 0.000 27 0.000 40 0.000 146 0.001 7 0.013 0.001 0.013999999999999999
19496 A19496-19496del|(ORF1ab_polyprotein:19232-19232del(6411fs)) 2 0.027 1 0.027 0 0.027
19497 T19497-19497del|(ORF1ab_polyprotein:19233-19233del(6411fs)) 1 0.015 1 0.015 0 0.015
19515 A19515G|(ORF1ab_polyprotein:A19251G(R6417R)) 1 0.016 15 0.000 27 0.000 42 0.000 7 0.000 32 0.000 13 0.000 7 0.016 0.0 0.016
19525 G19525T|(ORF1ab_polyprotein:GAT19261-19263TAG(D6421*)) 1 0.016 1 0.000 2 0.016 0.0 0.016
19527 T19527G|(ORF1ab_polyprotein:GAT19261-19263TAG(D6421*)) 1 0.016 1 0.000 2 0.016 0.0 0.016
19544 T19544C|(ORF1ab_polyprotein:T19280C(I6427T)) 1 0.016 15 0.000 12 0.000 35 0.000 10 0.000 15 0.000 19 0.000 7 0.016 0.0 0.016
19594 C19594G|(ORF1ab_polyprotein:C19330G(L6444V)) 1 0.015 20 0.000 17 0.000 26 0.000 10 0.000 9 0.000 58 0.000 7 0.015 0.0 0.015
19595 T19595C|(ORF1ab_polyprotein:T19331C(L6444P)) 1 0.015 20 0.000 34 0.000 49 0.000 21 0.000 28 0.000 30 0.000 7 0.015 0.0 0.015
19600 A19600T|(ORF1ab_polyprotein:AAC19336-19338TAG(N6446*)) 1 0.015 2 0.000 2 0.000 5 0.000 1 0.000 2 0.000 2 0.000 7 0.015 0.0 0.015
19602 C19602G|(ORF1ab_polyprotein:AAC19336-19338TAG(N6446*)) 1 0.015 2 0.000 2 0.000 5 0.000 1 0.000 2 0.000 2 0.000 7 0.015 0.0 0.015
19618 C19618A|(ORF1ab_polyprotein:CAG19354-19356ATG(Q6452M)) 1 0.015 2 0.000 3 0.000 8 0.000 1 0.000 5 0.000 13 0.000 7 0.015 0.0 0.015
19619 A19619T|(ORF1ab_polyprotein:CAG19354-19356ATG(Q6452M)) 1 0.015 2 0.000 3 0.000 8 0.000 1 0.000 5 0.000 13 0.000 7 0.015 0.0 0.015
19664 T19664A|(ORF1ab_polyprotein:T19400A(F6467Y)) 1 0.015 9 0.000 13 0.000 34 0.000 11 0.000 17 0.000 31 0.000 7 0.015 0.0 0.015
19664 T19664C|(ORF1ab_polyprotein:T19400C(F6467S)) 1 0.015 30 0.000 22 0.000 47 0.000 15 0.000 24 0.000 34 0.000 7 0.015 0.0 0.015
19677 G19677T|(ORF1ab_polyprotein:G19413T(Q6471H)) 1 0.015 56 0.000 66 0.000 89 0.000 24 0.000 35 0.000 106 0.001 7 0.015 0.001 0.016
19706 A19706T|(ORF1ab_polyprotein:A19442T(N6481I)) 1 0.015 46 0.000 63 0.000 118 0.000 28 0.000 48 0.000 126 0.001 7 0.015 0.001 0.016
19738 G19738T|(ORF1ab_polyprotein:G19474T(V6492L)) 1 0.011 18 0.000 15 0.000 31 0.000 4 0.000 18 0.000 89 0.000 7 0.011 0.0 0.011
19741 G19741T|(ORF1ab_polyprotein:G19477T(E6493*)) 1 0.011 24 0.000 34 0.000 74 0.000 28 0.000 30 0.000 97 0.000 7 0.011 0.0 0.011
linked 19955 C19955T|(ORF1ab_polyprotein:C19691T(T6564I)) 250939 0.991 51103 0.740 76095 0.997 71878 0.997 48644 0.997 59118 0.997 77107 0.997 11040 0.997 8 0.74 6.973 7.713
19990 G19990T|(ORF1ab_polyprotein:G19726T(D6576Y)) 235 0.001 18014 0.267 20 0.000 9 0.000 16 0.000 9 0.000 18 0.000 1 0.000 8 0.267 0.001 0.268
linked 20055 A20055G|(ORF1ab_polyprotein:A19791G(E6597E)) 248803 0.996 49974 0.743 75868 0.998 71476 0.998 48706 0.998 57961 0.998 76433 0.998 11050 0.998 8 0.743 6.984 7.727
20405 C20405T|(ORF1ab_polyprotein:C20141T(P6714L)) 5740 0.124 1 0.124 0 0.124
20745 T20745C|(ORF1ab_polyprotein:T20481C(N6827N)) 86954 0.247 2 0.000 5 0.000 5 0.000 2 0.000 2 0.000 2 0.000 7 0.247 0.0 0.247
21137 A21137G|(ORF1ab_polyprotein:A20873G(K6958R)) 189659 0.352 40 0.001 66 0.001 7 0.000 20 0.001 23 0.001 11 0.000 7 0.352 0.004 0.356
21497 T21497G|(ORF1ab_polyprotein:T21233G(L7078R)) 140 0.005 2 0.000 2 0.005 0.0 0.005
21540 T21540G|(ORF1ab_polyprotein:T21276G(V7092V)) 196 0.006 2 0.000 2 0.006 0.0 0.006
21542 T21542G|(ORF1ab_polyprotein:T21278G(L7093R)) 193 0.006 1 0.000 2 0.006 0.0 0.006
21543 T21543G|(ORF1ab_polyprotein:T21279G(L7093L)) 193 0.006 1 0.006 0 0.006
21564 T21564G|(surface_glycoprotein:T2G(M1R)) 259 0.008 1 0.008 0 0.008
21566 T21566G|(surface_glycoprotein:T4G(F2V)) 231 0.008 1 0.008 0 0.008
21567 T21567G|(surface_glycoprotein:T5G(F2C)) 456 0.015 4 0.001 2 0.015 0.001 0.016
21617 ACA21617-21619del|(surface_glycoprotein:55-57del(T19del)) 123891 0.997 1 0.997 0 0.997
21633 T21633C|(surface_glycoprotein:T71C(L24S)) 126514 0.997 1 0.997 0 0.997
21635 C21635T|(surface_glycoprotein:C73T(P25S)) 24088 0.190 1 0.19 0 0.19
21639 C21639T|(surface_glycoprotein:C77T(P26L)) 102372 0.806 1 0.806 0 0.806
21642 C21642A|(surface_glycoprotein:C80A(A27E)) 126688 0.997 1 0.997 0 0.997
21657 RATG13 T21657C|(surface_glycoprotein:T95C(F32S)) 24103 0.190 1 0.001 2 0.19 0.001 0.191
21707 C21707T|(surface_glycoprotein:C145T(H49Y)) 102878 0.996 1 0.996 0 0.996
21761 21761-insertA|(surface_glycoprotein:GCT199-201AGCGinsert(A67Sinsert;fs)) 103008 0.977 1 0.977 0 0.977
21763 T21763G|(surface_glycoprotein:GCT199-201AGCGinsert(A67Sinsert;fs)) 103008 0.977 1 0.977 0 0.977
21764 A21764C|(surface_glycoprotein:ATA202-204CNT(I68?)) 544 0.005 1 0.005 0 0.005
21764 A21764C|(surface_glycoprotein:ATA202-204CTT(I68L)) 102498 0.972 1 0.972 0 0.972
21766 A21766T|(surface_glycoprotein:ATA202-204CNT(I68?)) 544 0.005 1 0.005 0 0.005
21766 A21766T|(surface_glycoprotein:ATA202-204CTT(I68L)) 102498 0.972 1 0.972 0 0.972
21768 A21768-21768del|(surface_glycoprotein:206-206del(69fs)) 103622 0.982 1 0.982 0 0.982
21770 G21770A|(surface_glycoprotein:G208A(V70I)) 103500 0.981 1 0.981 0 0.981
21780 C21780A|(surface_glycoprotein:C218A(T73N)) 104657 0.991 1 0.991 0 0.991
21789 RATG13 C21789T|(surface_glycoprotein:C227T(T76I)) 104562 0.989 1 0.989 0 0.989
21811 C21811A|(surface_glycoprotein:C249A(V83V)) 105027 0.994 1 0.994 0 0.994
21823 T21823A|(surface_glycoprotein:T261A(N87K)) 104742 0.992 1 0.992 0 0.992
21984 TGGGTGTTTATTACCACAAAA21984-22004del|(surface_glycoprotein:TTGGGTGTTTATTACCACAAAAAC421-444TACdel(LGVYYHKN141-148Ydel)) 45454 0.986 1 0.986 0 0.986
22012 A22012T|(surface_glycoprotein:A450T(K150N)) 45700 0.988 27 0.000 31 0.000 6 0.000 10 0.000 1 0.000 6 0.988 0.0 0.988
22052 A22052C|(surface_glycoprotein:AAT490-492CAG(N164Q)) 253 0.005 7 0.000 12 0.000 2 0.000 1 0.000 1 0.000 6 0.005 0.0 0.005
22054 T22054G|(surface_glycoprotein:AAT490-492CAG(N164Q)) 253 0.005 7 0.000 12 0.000 2 0.000 1 0.000 1 0.000 6 0.005 0.0 0.005
22054 T22054G|(surface_glycoprotein:T492G(N164K)) 51685 0.985 56 0.001 75 0.001 19 0.001 11 0.000 3 0.000 6 0.985 0.003 0.988
22086 T22086C|(surface_glycoprotein:T524C(F175S)) 51838 0.988 20 0.000 11 0.000 4 0.000 4 0.000 2 0.000 6 0.988 0.0 0.988
22088 C22088T|(surface_glycoprotein:C526T(L176F)) 51989 0.990 3 0.000 3 0.000 1 0.000 1 0.000 5 0.99 0.0 0.99
22104 G22104T|(surface_glycoprotein:G542T(G181V)) 52008 0.991 41 0.000 38 0.000 13 0.000 7 0.000 5 0.000 6 0.991 0.0 0.991
22108 A22108C|(surface_glycoprotein:A546C(K182N)) 51798 0.987 19 0.000 41 0.000 6 0.000 4 0.000 1 0.000 6 0.987 0.0 0.987
22181 C22181T|(surface_glycoprotein:C619T(H207Y)) 51575 0.995 3 0.000 1 0.000 1 0.000 2 0.000 5 0.995 0.0 0.995
22189 TAT22189-22191del|(surface_glycoprotein:CCTATT625-630CCTdel(PI209-210Pdel)) 51278 0.414 7 0.000 20 0.000 4 0.000 2 0.000 5 0.414 0.0 0.414
22199 G22199T|(surface_glycoprotein:GTG637-639TCG(V213S)) 51488 0.413 1 0.413 0 0.413
22200 T22200C|(surface_glycoprotein:GTG637-639TCG(V213S)) 51488 0.413 1 0.413 0 0.413
22202 C22202G|(surface_glycoprotein:C640G(R214G)) 51470 0.412 12 0.000 7 0.000 2 0.000 2 0.000 1 0.000 6 0.412 0.0 0.412
22278 A22278G|(surface_glycoprotein:A716G(Q239R)) 373 0.005 8 0.000 3 0.000 5 0.000 9 0.000 7 0.000 6 0.005 0.0 0.005
ubiq 22295 C22295A|(surface_glycoprotein:C733A(H245N)) 73206 0.990 17055 0.998 36369 0.998 15443 0.998 15933 0.998 37765 0.998 71470 0.998 7 0.99 5.9879999999999995 6.978
22301 A22301G|(surface_glycoprotein:AGT739-741GAT(S247D)) 420 0.006 1 0.006 0 0.006
22302 G22302A|(surface_glycoprotein:AGT739-741GAT(S247D)) 420 0.006 1 0.006 0 0.006
22305 A22305C|(surface_glycoprotein:A743C(Y248S)) 447 0.006 8 0.000 12 0.000 3 0.000 2 0.000 10 0.000 7 0.000 7 0.006 0.0 0.006
22313 C22313T|(surface_glycoprotein:C751T(P251S)) 434 0.006 2 0.000 2 0.006 0.0 0.006
22320 ATTCTTCTT22320-22328del|(surface_glycoprotein:GATTCTTCTTCAGGT757-771GCTdel(DSSSG253-257Adel)) 427 0.006 1 0.006 0 0.006
22330 AGG22330-22332del|(surface_glycoprotein:GATTCTTCTTCAGGT757-771GCTdel(DSSSG253-257Adel)) 427 0.006 1 0.006 0 0.006
ubiq 22353 C22353A|(surface_glycoprotein:C791A(A264D)) 1 1.000 74025 0.986 17134 0.991 36482 0.989 15482 0.991 16019 0.992 37892 0.991 71991 0.990 8 0.986 6.944 7.93
22472 A22472C|(surface_glycoprotein:A910C(K304Q)) 442 0.006 1 0.000 3 0.000 1 0.000 1 0.000 3 0.000 6 0.000 7 0.006 0.0 0.006
22578 G22578A|(surface_glycoprotein:G1016A(G339D)) 11150 0.991 2 0.000 5 0.000 3 0.000 1 0.000 3 0.000 6 0.991 0.0 0.991
22582 A22582C|(surface_glycoprotein:A1020C(E340D)) 11133 0.990 13 0.000 28 0.000 13 0.000 2 0.000 2 0.000 6 0.99 0.0 0.99
22598 A22598G|(surface_glycoprotein:AGA1036-1038GAA(R346E)) 11108 0.988 1 0.988 0 0.988
22599 G22599A|(surface_glycoprotein:AGA1036-1038GAA(R346E)) 11108 0.988 1 0.988 0 0.988
22632 G22632A|(surface_glycoprotein:G1070A(R357K)) 11298 0.989 3 0.000 2 0.000 1 0.000 1 0.000 5 0.989 0.0 0.989
22674 C22674A|(surface_glycoprotein:C1112A(S371Y)) 11253 0.985 21 0.000 31 0.000 27 0.000 9 0.000 4 0.000 6 0.985 0.0 0.985
22696 G22696T|(surface_glycoprotein:G1134T(K378N)) 11244 0.986 14 0.000 12 0.000 13 0.000 4 0.000 2 0.000 6 0.986 0.0 0.986
22712 C22712T|(surface_glycoprotein:C1150T(P384S)) 11241 0.989 1 0.000 4 0.000 1 0.000 1 0.000 1 0.000 6 0.989 0.0 0.989
linkedubiq 22770 G22770A|(surface_glycoprotein:G1208A(R403K)) 1 1.000 10905 0.993 52490 0.998 71209 0.997 75565 0.998 21539 0.998 17347 0.998 7 0.993 5.989 6.982
linkedubiq 22775 G22775A|(surface_glycoprotein:G1213A(D405N)) 1 1.000 10935 0.990 52488 0.998 71315 0.997 75528 0.997 21597 0.998 20202 0.998 3108 1.000 8 0.99 6.9879999999999995 7.978
22799 G22799A|(surface_glycoprotein:GGG1237-1239AAG(G413K)) 10947 0.449 1 0.449 0 0.449
22800 G22800A|(surface_glycoprotein:GGG1237-1239AAG(G413K)) 10947 0.449 1 0.449 0 0.449
22812 A22812G|(surface_glycoprotein:A1250G(K417R)) 10950 0.449 1 0.449 0 0.449
ubiq 22882 T22882G|(surface_glycoprotein:T1320G(N440K)) 1 1.000 13369 0.965 2 1.000 101 0.990 56 1.000 2904 0.997 3202 0.998 7 0.965 5.985 6.95
22887 ATT22887-22889del|(surface_glycoprotein:GATTCT1324-1329GCTdel(DS442-443Adel)) 446 0.032 1 0.032 0 0.032
22893 AGGTTG22893-22898del|(surface_glycoprotein:AAGGTTGGT1330-1338AGTdel(KVG444-446Sdel)) 443 0.032 1 0.032 0 0.032
ubiq 22895 G22895C|(surface_glycoprotein:GTT1333-1335CGT(V445R)) 13479 0.960 102 1.000 1 0.018 16 0.005 3201 0.998 5 0.96 2.021 2.981
ubiq 22896 T22896G|(surface_glycoprotein:GTT1333-1335CGT(V445R)) 13479 0.960 102 1.000 1 0.018 16 0.005 3201 0.998 5 0.96 2.021 2.981
ubiq 22898 G22898A|(surface_glycoprotein:G1336A(G446S)) 1 1.000 13527 0.963 2 1.000 102 1.000 56 1.000 2903 0.997 3201 0.998 7 0.963 5.995 6.958
22901 G22901C|(surface_glycoprotein:GGTAATTAT1339-1347CGTdel(GNY447-449Rdel)) 395 0.028 1 0.028 0 0.028
22903 TAATTA22903-22908del|(surface_glycoprotein:GGTAATTAT1339-1347CGTdel(GNY447-449Rdel)) 395 0.028 1 0.028 0 0.028
ubiq 22910 A22910G|(surface_glycoprotein:A1348G(N450D)) 1 1.000 13566 0.962 2 1.000 102 1.000 56 1.000 2905 0.997 3202 0.998 7 0.962 5.995 6.957
ubiq 22916 C22916T|(surface_glycoprotein:CTG1354-1356TGG(L452W)) 1 1.000 13578 0.963 2 1.000 102 1.000 56 1.000 2906 0.998 3199 0.997 7 0.963 5.995 6.958
22917 T22917A|(surface_glycoprotein:T1355A(L452Q)) 447 0.032 1 0.032 0 0.032
ubiq 22917 Delta T22917G|(surface_glycoprotein:CTG1354-1356TGG(L452W)) 1 1.000 13578 0.963 2 1.000 102 1.000 56 1.000 2906 0.998 3199 0.997 7 0.963 5.995 6.958
22925 T22925G|(surface_glycoprotein:TTG1363-1365GCG(L455A)) 455 0.032 3 0.001 2 0.032 0.001 0.033
ubiq 22926 T22926C|(surface_glycoprotein:T1364C(L455S)) 1 1.000 13568 0.962 2 1.000 102 1.000 56 1.000 2921 0.997 3227 0.995 7 0.962 5.992 6.954
22926 T22926C|(surface_glycoprotein:TTG1363-1365GCG(L455A)) 455 0.032 3 0.001 2 0.032 0.001 0.033
ubiq 22928 T22928C|(surface_glycoprotein:T1366C(F456L)) 1 1.000 13547 0.961 101 0.990 56 1.000 2923 0.998 3223 0.994 6 0.961 4.982 5.9430000000000005
22936 G22936T|(surface_glycoprotein:G1374T(K458N)) 461 0.033 1 0.000 2 0.033 0.0 0.033
ubiq 22942 T22942A|(surface_glycoprotein:T1380A(N460K)) 1 1.000 13585 0.963 2 1.000 102 1.000 56 1.000 2918 0.996 3234 0.997 7 0.963 5.993 6.956
22942 T22942G|(surface_glycoprotein:T1380G(N460K)) 454 0.032 1 0.032 0 0.032
22979 T22979C|(surface_glycoprotein:T1417C(Y473H)) 453 0.032 2 0.001 1 0.000 3 0.032 0.001 0.033
22991 A22991G|(surface_glycoprotein:AGC1429-1431GAC(S477D)) 436 0.031 1 0.031 0 0.031
22992 G22992A|(surface_glycoprotein:AGC1429-1431GAC(S477D)) 436 0.031 1 0.031 0 0.031
ubiq 22992 G22992A|(surface_glycoprotein:G1430A(S477N)) 1 1.000 13383 0.966 2 1.000 100 0.990 1 0.018 16 0.006 3168 0.999 7 0.966 4.013 4.979
ubiq 22995 RATG13,Delta C22995A|(surface_glycoprotein:C1433A(T478K)) 1 1.000 13313 0.961 101 1.000 1 0.018 2885 0.994 3141 0.991 6 0.961 4.003 4.964
22997 C22997T|(surface_glycoprotein:C1435T(P479S)) 438 0.032 1 0.032 0 0.032
ubiq 23005 T23005A|(surface_glycoprotein:T1443A(N481K)) 1 1.000 13280 0.988 2 1.000 101 1.000 56 1.000 2886 0.994 3157 0.996 7 0.988 5.99 6.978
ubiq 23008 TGT23008-23010del|(surface_glycoprotein:GGTGTT1444-1449GGTdel(GV482-483Gdel)) 1 1.000 13265 0.987 2 1.000 101 1.000 55 0.982 2892 0.996 3153 0.994 7 0.987 5.9719999999999995 6.959
ubiq 23012 RATG13 G23012A|(surface_glycoprotein:G1450A(E484K)) 1 1.000 13322 0.991 2 1.000 101 1.000 55 0.982 2898 0.998 3161 0.997 7 0.991 5.977 6.968
ubiq 23018 RATG13 T23018C|(surface_glycoprotein:TTT1456-1458CCT(F486P)) 1 1.000 13354 0.994 2 1.000 101 1.000 56 1.000 2891 0.996 3156 0.995 7 0.994 5.991 6.984999999999999
ubiq 23019 T23019C|(surface_glycoprotein:TTT1456-1458CCT(F486P)) 1 1.000 13354 0.994 2 1.000 101 1.000 56 1.000 2891 0.996 3156 0.995 7 0.994 5.991 6.984999999999999
ubiq 23039 C23039G|(surface_glycoprotein:C1477G(Q493E)) 1 1.000 13352 0.993 2 1.000 101 1.000 1 0.018 16 0.006 3168 0.999 7 0.993 4.023 5.016
ubiq 23055 A23055G|(surface_glycoprotein:A1493G(Q498R)) 1 1.000 13369 0.994 2 1.000 100 0.990 56 1.000 2900 0.999 3168 0.999 7 0.994 5.9879999999999995 6.981999999999999
ubiq 23063 A23063T|(surface_glycoprotein:A1501T(N501Y)) 1 1.000 13354 0.993 2 1.000 101 1.000 55 0.982 2883 0.993 3158 0.996 7 0.993 5.971 6.964
ubiq 23075 RATG13 T23075C|(surface_glycoprotein:T1513C(Y505H)) 1 1.000 13377 0.995 2 1.000 99 1.000 56 1.000 2896 0.998 3168 0.998 7 0.995 5.996 6.9910000000000005
23130 C23130A|(surface_glycoprotein:C1568A(T523N)) 1326 0.010 33 0.000 47 0.000 29 0.000 27 0.000 27 0.000 60 0.001 7 0.01 0.001 0.011
23149 G23149T|(surface_glycoprotein:G1587T(K529N)) 1355 0.010 32 0.000 32 0.000 13 0.000 29 0.000 17 0.000 52 0.001 7 0.01 0.001 0.011
ubiq 23222 G23222A|(surface_glycoprotein:G1660A(E554K)) 1 1.000 132915 0.986 106918 0.998 136560 0.998 59932 0.998 99848 0.998 101016 0.998 77888 0.996 8 0.986 6.986 7.9719999999999995
23280 C23280T|(surface_glycoprotein:C1718T(T573I)) 6 0.000 16519 0.088 1 0.000 3 0.000 1 0.000 1 0.000 3 0.000 2 0.000 8 0.088 0.0 0.088
23336 T23336G|(surface_glycoprotein:T1774G(F592V)) 868 0.005 16772 0.090 62 0.001 69 0.000 68 0.001 164 0.001 138 0.001 44 0.001 8 0.09 0.01 0.09999999999999999
linkedubiq 23403 Delta A23403G|(surface_glycoprotein:A1841G(D614G)) 339469 0.992 226808 0.995 114633 0.999 142196 0.999 68146 0.999 119510 0.999 119687 0.999 84893 0.998 8 0.995 6.985 7.98
23427 T23427A|(surface_glycoprotein:GTT1864-1866GAC(V622D)) 29041 0.127 1 0.127 0 0.127
23428 T23428C|(surface_glycoprotein:GTT1864-1866GAC(V622D)) 29041 0.127 1 0.127 0 0.127
23429 G23429A|(surface_glycoprotein:G1867A(A623T)) 51 0.000 27182 0.119 3 0.000 10 0.000 4 0.000 8 0.000 11 0.000 6 0.000 8 0.119 0.0 0.119
23429 G23429A|(surface_glycoprotein:GCT1867-1869ACC(A623T)) 1809 0.008 1 0.008 0 0.008
23431 T23431C|(surface_glycoprotein:GCT1867-1869ACC(A623T)) 1809 0.008 1 0.008 0 0.008
23487 T23487G|(surface_glycoprotein:T1925G(V642G)) 46 0.000 14999 0.291 3 0.000 2 0.000 1 0.000 2 0.000 5 0.000 7 0.291 0.0 0.291
linkedubiq 23525 C23525T|(surface_glycoprotein:C1963T(H655Y)) 184968 0.997 51328 0.997 7543 0.999 5245 0.999 8160 0.999 19819 0.999 18760 0.998 6848 0.998 8 0.997 6.989 7.986
23592 A23592T|(surface_glycoprotein:A2030T(Q677L)) 208 0.001 14984 0.294 1 0.000 2 0.000 2 0.000 4 0.000 4 0.000 1 0.000 8 0.294 0.001 0.295
linkedubiq 23604 Delta C23604G|(surface_glycoprotein:C2042G(P681R)) 82 1.000 104102 0.999 105209 0.999 52632 0.999 38033 0.999 47502 0.999 50243 0.999 7 0.999 5.995 6.994
23638 RATG13 C23638T|(surface_glycoprotein:C2076T(I692I)) 104629 0.994 4 0.000 4 0.000 2 0.000 5 0.000 5 0.994 0.0 0.994
linked 23854 C23854A|(surface_glycoprotein:C2292A(N764K)) 104060 0.701 105069 0.997 52507 0.996 38023 0.997 48118 0.996 50575 0.996 6 0.701 4.982 5.683
23945 A23945G|(surface_glycoprotein:A2383G(K795E)) 44329 0.151 3 0.000 6 0.000 1 0.000 4 0.151 0.0 0.151
24044 C24044G|(surface_glycoprotein:C2482G(L828V)) 45209 0.151 7 0.000 6 0.000 3 0.000 4 0.151 0.0 0.151
24079 T24079G|(surface_glycoprotein:T2517G(D839E)) 44873 0.153 172 0.003 180 0.003 49 0.003 4 0.153 0.009000000000000001 0.162
24083 C24083T|(surface_glycoprotein:C2521T(L841F)) 44531 0.151 5 0.000 2 0.151 0.0 0.151
24090 A24090G|(surface_glycoprotein:A2528G(D843G)) 44479 0.151 11 0.000 3 0.000 3 0.151 0.0 0.151
24111 T24111C|(surface_glycoprotein:T2549C(I850T)) 44391 0.151 32 0.001 55 0.001 9 0.000 4 0.151 0.002 0.153
24333 C24333A|(surface_glycoprotein:C2771A(A924D)) 6 0.006 1 0.006 0 0.006
24334 C24334A|(surface_glycoprotein:C2772A(A924A)) 5 0.005 1 0.005 0 0.005
24375 24375-insertT|(surface_glycoprotein:2813insertT(938fs)) 1052 0.986 1 0.986 0 0.986
linkedubiq 24378 C24378T|(surface_glycoprotein:C2816T(S939F)) 1059 0.993 1320 0.995 303 1.000 393 0.995 584 0.997 831 0.998 6 0.993 4.985 5.978000000000001
linkedubiq 24424 A24424T|(surface_glycoprotein:A2862T(Q954H)) 1039 0.988 1310 0.995 297 0.987 390 0.992 582 1.000 825 0.995 6 0.988 4.969 5.957000000000001
linkedubiq 24469 T24469A|(surface_glycoprotein:T2907A(N969K)) 1060 0.971 1311 0.995 297 0.997 393 0.992 578 0.991 824 0.994 6 0.971 4.969 5.94
24712 G24712A|(surface_glycoprotein:G3150A(M1050I)) 80027 0.468 3 0.000 4 0.000 1 0.000 4 0.468 0.0 0.468
ubiq 24872 G24872T|(surface_glycoprotein:G3310T(V1104L)) 1 0.333 34738 0.995 40578 0.996 44704 0.996 30652 0.776 35941 0.997 6 0.995 4.098 5.093
ubiq 24990 C24990T|(surface_glycoprotein:C3428T(P1143L)) 3 1.000 35039 0.990 40582 0.996 44593 0.995 39340 0.996 35886 0.997 6 0.99 4.984 5.974
ubiq 25000 RATG13 C25000T|(surface_glycoprotein:C3438T(D1146D)) 1 1.000 34648 0.994 40446 0.993 44470 0.992 39258 0.994 35800 0.994 6 0.994 4.973 5.967
ubiq 25006 C25006T|(surface_glycoprotein:C3444T(F1148F)) 34723 0.996 1 0.000 9463 0.240 1 0.000 4 0.996 0.24 1.236
ubiq 25207 C25207T|(surface_glycoprotein:C3645T(Y1215Y)) 11151 0.992 5860 0.994 2254 0.995 3883 0.994 1538 0.995 5 0.992 3.9779999999999998 4.97
25216 A25216T|(surface_glycoprotein:A3654T(L1218L)) 53 0.005 1 0.000 1 0.000 3 0.005 0.0 0.005
ubiq 25584 C25584T|(ORF3a_protein:C192T(T64T)) 4 1.000 163807 0.994 2 1.000 74383 0.996 25259 0.997 76209 0.997 68671 0.995 7 0.994 5.985 6.979
25748 A25748G|(ORF3a_protein:A356G(N119S)) 1 0.007 1 0.000 2 0.007 0.0 0.007
25756 A25756C|(ORF3a_protein:A364C(R122R)) 1 0.031 2 0.000 2 0.001 2 0.000 4 0.031 0.001 0.032
26338 GC26338-26339del|(envelope_protein:94-95del(32fs)) 1 0.167 1 0.167 0 0.167
26340 26340-insertA|(envelope_protein:96insertA(32fs)) 1 0.012 1 0.000 2 0.012 0.0 0.012
26354 T26354C|(envelope_protein:T110C(L37P)) 1 0.010 1 0.000 1 0.000 1 0.000 5 0.000 5 0.01 0.0 0.01
26361 G26361T|(envelope_protein:G117T(L39F)) 1 0.008 2 0.000 1 0.000 1 0.000 16 0.000 5 0.008 0.0 0.008
26363 G26363C|(envelope_protein:G119C(C40S)) 1 0.008 1 0.008 0 0.008
26366 C26366A|(envelope_protein:C122A(A41E)) 2 0.015 1 0.000 2 0.001 1 0.000 1 0.000 38 0.001 6 0.015 0.002 0.017
linked 26421 C26421G|(envelope_protein:C177G(Y59*)) 117 0.000 22 0.000 15 0.000 4 0.000 5 0.000 16 0.000 6 0.0 0.0 0.0
linked 26488 T26488G 437 0.002 152 0.002 112 0.003 1 0.004 46 0.002 90 0.002 209 0.002 7 0.002 0.015 0.017
linked 26492 A26492G 75 0.000 28 0.000 22 0.001 5 0.000 8 0.000 362 0.003 6 0.0 0.004 0.004
ubiq 26529 G26529C|(membrane_glycoprotein:G7C(D3H)) 3 1.000 289399 0.988 74285 0.994 38183 0.993 235 0.996 20274 0.993 37559 0.994 125825 0.992 8 0.988 6.962 7.949999999999999
linked 26529 G26529C|(membrane_glycoprotein:GAT7-9CTT(D3L)) 141 0.000 5 0.000 6 0.000 3 0.000 5 0.000 8 0.000 6 0.0 0.0 0.0
linked 26530 A26530T|(membrane_glycoprotein:GAT7-9CTT(D3L)) 141 0.000 5 0.000 6 0.000 3 0.000 5 0.000 8 0.000 6 0.0 0.0 0.0
ubiq 26577 C26577G|(membrane_glycoprotein:C55G(Q19E)) 3 1.000 289931 0.991 74245 0.994 38154 0.993 235 0.996 20171 0.993 37507 0.995 125802 0.993 8 0.991 6.964 7.955
ubiq 26610 A26610G|(membrane_glycoprotein:A88G(T30A)) 2 0.667 285782 0.992 74457 0.997 38292 0.997 235 0.996 20239 0.997 37573 0.997 126050 0.995 8 0.992 6.646 7.638
ubiq 26681 C26681T|(membrane_glycoprotein:C159T(F53F)) 3 1.000 287618 0.998 74619 0.999 44685 0.998 2137 1.000 35762 0.998 58215 0.998 161828 0.999 8 0.998 6.992 7.99
ubiq 26709 G26709A|(membrane_glycoprotein:G187A(A63T)) 2 0.667 287027 0.996 74607 0.999 44665 0.997 2124 0.993 35807 0.997 58169 0.997 161673 0.997 8 0.996 6.647 7.643000000000001
27005 C27005T|(membrane_glycoprotein:C483T(I161I)) 31989 0.291 1 0.000 2 0.000 2 0.000 2 0.000 2 0.000 5 0.000 7 0.291 0.0 0.291
27008 G27008T|(membrane_glycoprotein:G486T(K162N)) 32158 0.293 42 0.001 42 0.001 22 0.001 23 0.001 19 0.000 194 0.002 7 0.293 0.006 0.299
27056 T27056C|(membrane_glycoprotein:T534C(Y178Y)) 32005 0.291 13 0.000 10 0.000 2 0.000 1 0.000 5 0.000 6 0.000 7 0.291 0.0 0.291
27112 G27112C|(membrane_glycoprotein:G590C(S197T)) 32313 0.293 6 0.000 2 0.000 2 0.000 1 0.000 7 0.000 6 0.293 0.0 0.293
27147 G27147A|(membrane_glycoprotein:G625A(D209N)) 32155 0.288 11 0.000 15 0.000 7 0.000 4 0.000 5 0.000 40 0.000 7 0.288 0.0 0.288
27192 GTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTAC27192-27230del|(ORF6_protein:Start_disrupted) 30708 0.285 1 0.285 0 0.285
27233 T27233C|(ORF6_protein:T32C(I11T)) 30751 0.141 8 0.000 24 0.000 9 0.000 9 0.000 12 0.000 12 0.000 7 0.141 0.0 0.141
27242 T27242C|(ORF6_protein:T41C(I14T)) 67 0.000 154461 0.451 13 0.000 16 0.000 1 0.000 4 0.000 7 0.000 11 0.000 8 0.451 0.0 0.451
27262 A27262G|(ORF6_protein:A61G(T21A)) 112 0.000 153992 0.449 5 0.000 23 0.000 3 0.000 7 0.000 7 0.000 15 0.000 8 0.449 0.0 0.449
27266 T27266C|(ORF6_protein:T65C(F22S)) 98 0.000 30680 0.089 10 0.000 15 0.000 4 0.000 8 0.000 8 0.000 16 0.000 8 0.089 0.0 0.089
27285 RATG13 T27285C|(ORF6_protein:T84C(N28N)) 83 0.000 124033 0.362 7 0.000 17 0.000 2 0.000 5 0.000 11 0.000 14 0.000 8 0.362 0.0 0.362
27290 A27290G|(ORF6_protein:A89G(D30G)) 103 0.000 154338 0.450 6 0.000 14 0.000 4 0.000 10 0.000 5 0.000 12 0.000 8 0.45 0.0 0.45
27292 T27292C|(ORF6_protein:T91C(Y31H)) 103 0.000 30714 0.090 4 0.000 22 0.000 6 0.000 9 0.000 11 0.000 17 0.000 8 0.09 0.0 0.09
ubiq 27382 G27382C|(ORF6_protein:GAT181-183CTC(D61L)) 580358 0.994 113211 0.993 67496 0.998 27818 0.998 36346 0.998 71051 0.996 6 0.993 4.984 5.977
ubiq 27383 A27383T|(ORF6_protein:GAT181-183CTC(D61L)) 580358 0.994 113211 0.993 67496 0.998 27818 0.998 36346 0.998 71051 0.996 6 0.993 4.984 5.977
ubiq 27384 T27384C|(ORF6_protein:GAT181-183CTC(D61L)) 580358 0.994 113211 0.993 67496 0.998 27818 0.998 36346 0.998 71051 0.996 6 0.993 4.984 5.977
ubiq 27807 C27807T|(ORF7b:C52T(L18L)) 6 1.000 331611 0.995 70517 0.997 86981 0.996 44732 0.997 69580 0.996 65256 0.997 138510 0.998 8 0.995 6.981 7.976
ubiq 27810 T27810C|(ORF7b:T55C(F19L)) 6 1.000 331534 0.995 70616 0.998 87135 0.997 44799 0.998 69695 0.998 65331 0.998 138304 0.996 8 0.995 6.985 7.98
ubiq 28271 A28271T 7 1.000 356652 0.997 1 1.000 110207 0.998 300216 0.998 163572 0.998 160502 0.998 103482 0.998 8 0.997 6.99 7.987
ubiq 28311 C28311T|(nucleocapsid_phosphoprotein:C38T(P13L)) 12 0.923 361154 0.995 1 1.000 110297 0.998 300345 0.998 163663 0.998 160604 0.998 103521 0.998 8 0.995 6.913 7.908
ubiq 28362 GAGAACGCA28362-28370del|(nucleocapsid_phosphoprotein:GGAGAACGCAGT88-99GGTdel(GERS30-33Gdel)) 11 1.000 359785 0.993 1 1.000 110012 0.998 300234 0.998 163172 0.998 160224 0.999 103464 0.998 8 0.993 6.991 7.984
ubiq 28881 G28881A|(nucleocapsid_phosphoprotein:AGG607-609AAA(R203K)) 140661 0.997 42342 0.996 69617 0.997 76212 0.997 38110 0.996 63231 0.998 49065 0.998 7 0.997 5.982 6.979
ubiq 28882 G28882A|(nucleocapsid_phosphoprotein:AGG607-609AAA(R203K)) 140661 0.997 42342 0.996 69617 0.997 76212 0.997 38110 0.996 63231 0.998 49065 0.998 7 0.997 5.982 6.979
ubiq 28883 G28883C|(nucleocapsid_phosphoprotein:G610C(G204R)) 140660 0.997 42424 0.998 69658 0.997 72185 0.944 38157 0.998 56802 0.896 49087 0.998 7 0.997 5.8309999999999995 6.827999999999999
ubiq 28958 C28958A|(nucleocapsid_phosphoprotein:C685A(Q229K)) 140967 0.997 42438 0.998 69796 0.998 63051 0.824 33326 0.870 55352 0.872 49122 0.998 7 0.997 5.56 6.5569999999999995
29709 T29709G 157624 0.506 24 0.000 83 0.000 75 0.000 33 0.000 36 0.000 16 0.000 7 0.506 0.0 0.506
29734 G29734C 152872 0.497 1 0.000 3 0.000 1 0.000 4 0.497 0.0 0.497
29736 GGCCACGCGGAGTACGATCGAGTG29736-29759del 154432 0.502 2 0.000 2 0.000 1 0.000 4 0.502 0.0 0.502