61
genetics / spike-mutations
« on: December 22, 2020, 12:42:56 pm »Code: [Select]
29, 26, 1,C21575T, L5F,
937, 435, 36,C21614T, L18F,20A.EU1=B.1.177
9, 10, 0,C21627T, T22I,
31, 11, 0,A21631T, Q23H,
41, 17, 7,C21637T, ,
6, 7, 0,C21638T, P26S,
2, 6, 0,C21727T, ,
30, 6, 5,G21800T, D80Y,
9, 10, 0,C21855T, S98F,
0, 6, 0,C22000T, ,
2, 6, 0,T22016A, W152R,
81, 6, 0,G22051T, ,
15, 6, 8,A22053C, N164T,
7, 8, 3,C22075T, ,
18, 7, 0,C22088T, L176F,
7, 9, 3,G22131T, R190M,
15, 19, 0,G22205C, D215H,
16, 11, 0,C22224T, S221L,
1584, 908, 73,C22227T, A222V,20A.EU1=B.1.177
13, 10, 0,C22329T, S256L,
58, 52, 3,G22346T, A262S, B.1.177
39, 39, 0,C22377T, P272L,
20, 13, 1,C22388T, ,
0, 19, 0,C22432T, ,
63, 47, 2,C22444T, , B.1.36
1, 8, 0,C22530T, T323I,
1, 7, 1,A22546G, ,
36, 33, 3,C22879A, N439K, B.1.5
2, 13, 1,G22918T, ,
43, 16, 0,G22992A, S477N,
6, 10, 0,T23042C, S494P,
423, 880, 12,A23063T, N501Y, B.1.1.7
406, 885, 14,C23271A, A570D, B.1.1.7
42, 25, 4,G23311C, E583D,
6, 19, 3,T23323C, ,
9, 6, 0,G23401T, Q613H,
2344,2015, 104,A23403G, D614G,
409, 889, 14,C23604A, P681H, B.1.1.7
1, 6, 0,G23608T, ,
12, 10, 0,C23625T, A688V,
28, 24, 0,C23644T, ,
11, 11, 0,C23679T, A706V,
407, 883, 14,C23709T, T716I, B.1.1.7
0, 6, 0,T23866C, ,
5, 14, 1,G23873T, A771S,
21, 10, 0,T24088C, ,
19, 35, 1,C24106T, ,
1, 6, 0,C24130T, ,
1, 6, 0,C24138A, T859N,
4, 9, 0,C24138T, T859I,
347, 235, 16,C24334T, ,
7, 15, 0,C24378T, S939F,
32, 9, 0,C24382T, ,
406, 885, 14,T24506G, S982A, B.1.1.7
11, 8, 0,G24620T,A1020S,
14, 10, 0,T24769C, ,
3, 8, 0,G24781T,K1073N,
30, 19, 1,T24910C, ,
406, 887, 14,G24914C,D1118H, B.1.1.7
1, 8, 1,T24979C, ,
4, 6, 0,C25000T, ,
2, 7, 0,G25049K, ,
45, 71, 0,G25049T,D1163Y, B.1.177
46, 76, 0,G25062T,G1167V, B.1.177
12, 14, 0,C25096T, ,
4, 14, 1,C25349A,P1263T,
-----------------------------------------------------
2345,2027,0104,total genomes
0049,0050,0051,week
frequency of spike-mutations in 133277 full genomes
in week 50 from cogconsortium , 2020/12/22
831,45416,151499
checking for the new strain B.1.1.7 = VUI202012/01 = VOC2020
prevalence in UK : http://magictour.free.fr/b117a.GIF
2020/12/08 , genbank=5/44708 , UK=1203(1050)/131631
2020/12/15 , DE=0/747 , UK=1289/133960
2020/12/17 , DE=0/764 , UK=141600 new strain-names
2020/12/20 , UK=2100/146416
2020/12/21 , DE=0/834,UK=3042/150173
2020/12/22 , DE=834,genbank=,UK=3063/150399
2020/12/23 , DE=0/831,genbank=45416,UK=3094/151499,RKI:0/1742
I downloaded the 133277 aligned sequences from cogconsortium (3.9GB)
and processed/converted them into a better format :
http://magictour.free.fr/sars2uk8.7z (2MB)
this takes many hours each day for me , because of the big files.
Is someone else doing this ?
Can we coordinate, exchange the processed/improved data ?
-------------------------------------------
viruses with many spike-amino-acid mutations :
genbank, USA,CA : S13I,C136G,W152C,L452R
UK, B.1.1.7 , B.1.258 , B.1.37 , B.1.315 , B.1.177 , B.1.160 , B.1.5 , B.1.351 (SA)
file spisur.12a : sequences with >=5? spike-amino-acid-mutations (2020/12/28)
Code: [Select]
182,B.1.177.9
55,B.1.177
31,B.1.258.4
25,B.1.1.37
14,B.1.177.6
11,B.1.177.17
4,B.1.1
3,B.1.160.7
1,B.1.5.34
1,B.1.351
1,B.1.1.194
Code: [Select]
329,D614G
286,A222V
222,A262S
184,D80Y
183,N164T
127,E583D
57,L5F
46,L18F
40,P272L
32,G1219V
31,V772I
31,N439K
31,L189F
28,H655Y
27,T95I
25,D574Y
18,V308L
15,Q23H
15,A1020S
12,I1216V
11,L176F
8,N536S
8,G446V
8,D796H
8,A520S
7,G1167V
7,D1163Y
6,Q613H
6,D215H
5,S98F
5,S477N
5,R346K
4,K1205N
4,A1226V
3,W152R
3,T678I
3,S884F
3,S221L
3,R21K
3,P681L
3,L244F
3,G482S
3,F329L
3,A871S
2,T716I
2,S982A
2,R190K
2,Q677H
2,Q675R
2,Q218H
2,P681H
2,P384L
2,N501Y
2,L552F
2,L1141F
2,K1191N
2,H146Y
2,E484K
2,E1150D
2,D936Y
2,D215Y
2,D215V
2,D138Y
2,D1118H
2,A845S
2,A783T
2,A771S
2,A706V
2,A688V
2,A570D
2,A522V
2,A522S
2,A1174V
2,A1078S
1,Y269C
1,Y266C
1,Y200C
1,Y145N
1,V687L
1,V539I
1,V445I
1,V36L
1,V367F
1,V213A
1,V1230A
1,V1104L
1,T768N
1,T63N
1,T51I
1,T307N
1,T22I
1,T20I
1,T19K
1,S937L
1,S813I
1,S735A
1,S691F
1,S659L
1,S50L
1,S494P
1,S151T
1,S12F
1,S1261F
1,S1242I
1,S1175P
1,R765L
1,R214L
1,Q314K
1,P9L
1,P681R
1,P561T
1,P384S
1,P1079S
1,N925S
1,N556Y
1,N211T
1,L822F
1,L455F
1,L216F
1,L141F
1,K444R
1,K417N
1,K1181I
1,K1073N
1,I468V
1,I210T
1,I1179V
1,H146Q
1,G482A
1,G476F
1,G181V
1,G181A
1,G142V
1,G1124V
1,F2L
1,F157S
1,F157L
1,E484R
1,E1182Q
1,D80A
1,D215G
1,D1257Y
1,D1153Y
1,D1084Y
1,A924V
1,A924S
1,A879V
1,A846V
1,A701V
1,A668S
1,A653V
1,A647S
1,A27S
1,A243S
1,A163V