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Tables of mutating sites in Spike, updated daily

Last update: Oct 21, 2021


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Table 1A. Table of sites with common mutations, found with a frequency of >0.003. (Within the ACE2 contact region, the frequency threshold for inclusion is lower, >0.001.)

Note: The mutation D614G is not included in this summary; it is now the globally dominant form and can be readily tracked using many other tools at this site.

total # of seqs: 3246301

oriposmutglobal countglobal frequency
L5#4350.0001340
-1470.0000453
C10.0000003
F962780.0296578
I230.0000071
P40.0000012
R10.0000003
V30.0000009
X22320.0006876
S13#40.0000012
-20.0000006
C280.0000086
G970.0000299
I325790.0100357
N1360.0000419
R30.0000009
T4680.0001442
V10.0000003
X12520.0003857
L18#20.0000006
-450.0000139
F1579160.0486449
H50.0000015
I270.0000083
K80.0000025
P260.0000080
R27700.0008533
S10.0000003
V70.0000022
X9510.0002929
T19#30.0000009
-70.0000022
A750.0000231
G560.0000173
I21700.0006685
K2290.0000705
P60.0000018
Q10.0000003
R12835540.3953897
S430.0000132
X10780.0003321
T20-250.0000077
A1820.0000561
F30.0000009
I77990.0024024
K100.0000031
N759020.0233811
P1370.0000422
S950.0000293
X3440.0001060
P26#280.0000086
-40.0000012
A20.0000006
F800.0000246
H3640.0001121
L21830.0006725
R1240.0000382
S833110.0256634
T370.0000114
X3810.0001174
Y50.0000015
T29-30.0000009
A67310.0020734
H10.0000003
I31900.0009827
N10.0000003
P20.0000006
R10.0000003
S1110.0000342
V70.0000022
W10.0000003
X1810.0000558
A67#20.0000006
-160.0000049
D2070.0000638
F10.0000003
G200.0000062
M10.0000003
N50.0000015
P130.0000040
S33850.0010427
T1200.0000370
V137880.0042473
X5530.0001703
H69-9885160.3045053
A40.0000012
D230.0000071
I40.0000012
L410.0000126
M20.0000006
N190.0000059
P200.0000062
Q1400.0000431
R780.0000240
S3120.0000961
T20.0000006
X187520.0057764
Y18810.0005794
V70#30980.0009543
-9845500.3032836
A1120.0000345
D10.0000003
E10.0000003
F46990.0014475
G1950.0000601
I68170.0020999
K10.0000003
L2030.0000625
M10.0000003
X146210.0045039
G75-610.0000188
A3200.0000986
C750.0000231
D1440.0000444
F30.0000009
I10.0000003
K60.0000018
R22850.0007039
S2660.0000819
T10.0000003
V100550.0030974
X6410.0001975
K77$20.0000006
-400.0000123
E100.0000031
F10.0000003
I60.0000018
M510.0000157
N5650.0001740
R730.0000225
T100390.0030924
X2900.0000893
D80#20.0000006
-60.0000018
A122580.0037760
C100.0000031
E220.0000068
F270.0000083
G105530.0032508
H950.0000293
K10.0000003
L10.0000003
N3010.0000927
P10.0000003
S30.0000009
T10.0000003
V110.0000034
X4490.0001383
Y73240.0022561
T95#100.0000031
$10.0000003
-150.0000046
A1100.0000339
F90.0000028
I6278330.1933995
M60.0000018
N2290.0000705
P10.0000003
S880.0000271
V430.0000132
X22260.0006857
S98-40.0000012
A60.0000018
C10.0000003
F335780.0103435
N10.0000003
P920.0000283
R10.0000003
T110.0000034
X6620.0002039
Y180.0000055
S112$20.0000006
-110.0000034
A190.0000059
F290.0000089
L269320.0082962
M60.0000018
P1150.0000354
T130.0000040
X9910.0003053
D138#30.0000009
-2880.0000887
A1960.0000604
E80.0000025
G2670.0000822
H174800.0053846
N3790.0001167
V270.0000083
X14750.0004544
Y828420.0255189
G142#950.0000293
-28230.0008696
A490.0000151
C700.0000216
D9760480.3006647
E10.0000003
F70.0000022
H100.0000031
I70.0000022
K20.0000006
L30.0000009
N210.0000065
P40.0000012
R30.0000009
S9440.0002908
T40.0000012
V28430.0008758
W20.0000006
X823670.0253726
Y660.0000203
Y144#21890.0006743
$150.0000046
-9707600.2990357
C200.0000062
D40.0000012
E20.0000006
F12400.0003820
G20.0000006
H530.0000163
K90.0000028
L50.0000015
N740.0000228
S68410.0021073
T1700.0000524
V3200.0000986
W40.0000012
X244870.0075430
Y145#820.0000253
$70.0000022
-7190.0002215
C210.0000065
D1040.0000320
F10.0000003
G10.0000003
H151750.0046746
N73170.0022539
P10.0000003
S330.0000102
T10.0000003
X54310.0016730
W152#20.0000006
$10.0000003
-480.0000148
C316400.0097465
F40.0000012
G960.0000296
K10.0000003
L106570.0032828
Q20.0000006
R180900.0055725
S350.0000108
X9000.0002772
Y10.0000003
M153#90.0000028
-420.0000129
I39500.0012168
K1750.0000539
L260.0000080
R40.0000012
T87470.0026945
V2790.0000859
W80.0000025
X4220.0001300
E156#430.0000132
$10.0000003
-5900.0001817
A790.0000243
D2400.0000739
F10.0000003
G12557700.3868310
K150.0000046
Q1430.0000441
S10.0000003
V7450.0002295
W10.0000003
X204840.0063100
Y20.0000006
F157#50.0000015
-12579270.3874955
C150.0000046
E10.0000003
L27120.0008354
S110580.0034063
V30.0000009
X247870.0076355
Y140.0000043
R158#1470.0000453
$1860.0000573
-12521690.3857218
G12240.0003770
I290.0000089
K390.0000120
L30.0000009
S28610.0008813
X288010.0088719
Y10.0000003
G181#30.0000009
$20.0000006
-20.0000006
A7240.0002230
E8860.0002729
K10.0000003
L480.0000148
N40.0000012
R13630.0004199
V82150.0025306
X3530.0001087
R190#100.0000031
-400.0000123
G440.0000136
I120.0000037
K2840.0000875
M2980.0000918
N140.0000043
S755990.0232877
T30.0000009
W400.0000123
X4500.0001386
D215#20.0000006
-120.0000037
A1320.0000407
C20.0000006
E1640.0000505
G123130.0037929
H27610.0008505
L50.0000015
N1830.0000564
V1000.0000308
X3770.0001161
Y43980.0013548
A222#40.0000012
-20.0000006
D30.0000009
F210.0000065
G10.0000003
I110.0000034
L10.0000003
N10.0000003
P770.0000237
R10.0000003
S15150.0004667
T640.0000197
V2912950.0897314
W10.0000003
X16680.0005138
L242#60.0000018
-126980.0039115
F2930.0000903
H280.0000086
I760.0000234
P1040.0000320
Q80.0000025
R30.0000009
V50.0000015
X8450.0002603
Y10.0000003
A243#930.0000286
-133870.0041238
D70.0000022
G330.0000102
P340.0000105
S20390.0006281
T610.0000188
V4110.0001266
X11340.0003493
L244#100.0000031
-135260.0041666
F840.0000259
S6340.0001953
V220.0000068
X1870.0000576
T250-61220.0018858
A560.0000173
F10.0000003
G40.0000012
I71760.0022105
N5750.0001771
P300.0000092
S7060.0002175
X1120.0000345
P251#880.0000271
-61110.0018825
H4580.0001411
L123340.0037994
R50.0000015
S8280.0002551
T1690.0000521
X1560.0000481
D253-61270.0018874
A16030.0004938
E120.0000037
G367860.0113317
H100.0000031
N1770.0000545
S120.0000037
V640.0000197
X2720.0000838
Y7010.0002159
A262#70.0000022
-130.0000040
D360.0000111
F10.0000003
G240.0000074
K10.0000003
P1580.0000487
S158170.0048723
T1240.0000382
V5730.0001765
W10.0000003
X20530.0006324
Y60.0000018
P272F310.0000095
H950.0000293
L96550.0029742
Q20.0000006
R60.0000018
S3500.0001078
T420.0000129
X4330.0001334
V289#10.0000003
A50.0000015
E10.0000003
I172200.0053045
L7860.0002421
T10.0000003
X3290.0001013
R346$10.0000003
F20.0000006
G1090.0000336
I3070.0000946
K85770.0026421
S16390.0005049
T930.0000286
X4600.0001417
K417#20.0000006
-10.0000003
A30.0000009
E110.0000034
M140.0000043
N152950.0047115
Q30.0000009
R1890.0000582
T738830.0227591
X11210.0003453
N439-20.0000006
D10.0000003
F10.0000003
I70.0000022
K269850.0083125
S30.0000009
T20.0000006
X5490.0001691
Y10.0000003
G446-10.0000003
A530.0000163
C10.0000003
D260.0000080
F10.0000003
I20.0000006
R90.0000028
S2650.0000816
T20.0000006
V35780.0011022
X10340.0003185
L452#120.0000037
-20.0000006
F10.0000003
H10.0000003
M12050.0003712
P20.0000006
Q69350.0021363
R13413910.4132060
V60.0000018
W410.0000126
X10660.0003284
S477#30.0000009
G4570.0001408
H10.0000003
I27590.0008499
K30.0000009
N583980.0179891
R12580.0003875
T340.0000105
V10.0000003
X8290.0002554
T478-30.0000009
A120.0000037
E10.0000003
I7170.0002209
K13041180.4017243
L10.0000003
N120.0000037
R4280.0001318
S20.0000006
X7180.0002212
E484#50.0000015
-20.0000006
A2820.0000869
D1000.0000308
G1130.0000348
K1522490.0468992
Q73290.0022576
R190.0000059
V410.0000126
X7040.0002169
F490$10.0000003
A10.0000003
I290.0000089
L8850.0002726
N10.0000003
S105440.0032480
V1090.0000336
X2390.0000736
Y920.0000283
S494#20.0000006
$10.0000003
-10.0000003
A510.0000157
L7000.0002156
P97050.0029896
Q10.0000003
R50.0000015
T120.0000037
X2540.0000782
N501#50.0000015
-170.0000052
D10.0000003
E10.0000003
F20.0000006
H380.0000117
I470.0000145
K130.0000040
L10.0000003
P20.0000006
Q20.0000006
R10.0000003
S940.0000290
T37370.0011512
X19990.0006158
Y10773030.3318555
A570D9726260.2996105
E10.0000003
G180.0000055
H10.0000003
N10.0000003
S18430.0005677
T300.0000092
V5310.0001636
X12150.0003743
Y1210.0000373
T572#40.0000012
A290.0000089
I108990.0033574
N840.0000259
S680.0000209
X1740.0000536
Q613$30.0000009
-10.0000003
E910.0000280
H200220.0061676
K320.0000099
L90.0000028
R500.0000154
X1980.0000610
Y20.0000006
H655-10.0000003
D10.0000003
E10.0000003
L220.0000068
N30.0000009
P120.0000037
Q200.0000062
R870.0000268
X3730.0001149
Y818870.0252247
Q675$20.0000006
-670.0000206
E20.0000006
H231570.0071333
K3190.0000983
L570.0000176
P110.0000034
R20480.0006309
S20.0000006
W20.0000006
X2270.0000699
Y30.0000009
Q677#10.0000003
-730.0000225
E30.0000009
H359330.0110689
K1220.0000376
L1690.0000521
P40650.0012522
R4840.0001491
S10.0000003
X5060.0001559
Y160.0000049
P681#140.0000043
-240.0000074
A10.0000003
C40.0000012
H10292100.3170408
L6480.0001996
Q10.0000003
R12977870.3997741
S780.0000240
T40.0000012
X23390.0007205
Y1050.0000323
A688-100.0000031
D270.0000083
F50.0000015
G80.0000025
P140.0000043
S7570.0002332
T4390.0001352
V127260.0039202
X2640.0000813
A701#20.0000006
-10.0000003
E100.0000031
G250.0000077
I10.0000003
K10.0000003
L10.0000003
P260.0000080
Q10.0000003
S11380.0003506
T1490.0000459
V416510.0128303
X3330.0001026
T716-20.0000006
A120.0000037
D10.0000003
I9787870.3015084
K60.0000018
L110.0000034
M70.0000022
N10.0000003
P10.0000003
Q10.0000003
R30.0000009
S110.0000034
V3340.0001029
X14730.0004537
T732-10.0000003
A237100.0073037
I13760.0004239
N20.0000006
S9520.0002933
V20.0000006
X1870.0000576
G769$10.0000003
-10.0000003
A1710.0000527
C10.0000003
E250.0000077
K100.0000031
N20.0000006
R3190.0000983
V129090.0039765
X1720.0000530
A845#10.0000003
-10.0000003
D730.0000225
G110.0000034
P280.0000086
R10.0000003
S89300.0027508
T890.0000274
V10400.0003204
X4030.0001241
T859#20.0000006
-60.0000018
A420.0000129
C10.0000003
I45630.0014056
N174680.0053809
S90.0000028
X2620.0000807
D936-20.0000006
A110.0000034
E1270.0000391
G1020.0000314
H13550.0004174
L10.0000003
N38960.0012001
T30.0000009
V960.0000296
X1970.0000607
Y51600.0015895
S939#20.0000006
-30.0000009
A140.0000043
C20.0000006
F100290.0030894
P10.0000003
T30.0000009
X2080.0000641
Y610.0000188
D950#910.0000280
-10.0000003
A240.0000074
E100.0000031
G340.0000105
H101700.0031328
I80.0000025
K40.0000012
N12414580.3824223
S170.0000052
T30.0000009
V20.0000006
W10.0000003
X321870.0099150
Y1880.0000579
Q957$10.0000003
-10.0000003
A20.0000006
E150.0000046
H380.0000117
K30.0000009
L10720.0003302
N10.0000003
R106040.0032665
X16430.0005061
S982#10.0000003
A9728070.2996663
L1080.0000333
P10.0000003
T50.0000015
V10.0000003
X13760.0004239
T1027-10.0000003
A270.0000083
I842110.0259406
N250.0000077
S450.0000139
V70.0000022
X2360.0000727
A1078#10.0000003
D10.0000003
F10.0000003
S93640.0028845
T5100.0001571
V5860.0001805
X2380.0000733
V1104#40.0000012
$10.0000003
-10.0000003
A120.0000037
E10.0000003
I4980.0001534
L175710.0054126
X1750.0000539
D1118#10.0000003
A390.0000120
E90.0000028
G250.0000077
H9717460.2993395
N20.0000006
Q40.0000012
R40.0000012
V220.0000068
X15470.0004765
Y32310.0009953
P1162A2590.0000798
L28220.0008693
Q680.0000209
R5980.0001842
S68480.0021095
T590.0000182
X2980.0000918
V1176-10.0000003
A40.0000012
D10.0000003
F870070.0268019
G30.0000009
I320.0000099
L100.0000031
X2290.0000705
K1191-10.0000003
D10.0000003
E180.0000055
M70.0000022
N338270.0104202
Q400.0000123
R340.0000105
T90.0000028
X4440.0001368
G1219A300.0000092
C45570.0014038
D60.0000018
F40.0000012
L10.0000003
R60.0000018
S1620.0000499
V69390.0021375
X2420.0000745
Y10.0000003
V1264-10.0000003
A600.0000185
D30.0000009
E50.0000015
F620.0000191
G40.0000012
L343980.0105961
M810.0000250
S10.0000003
X5110.0001574


Table 1B. Details regarding common mutations listed in A and their geographic locations.


oriposmutcodonmutcovariationslocation# of occurrences#seqs from local#seqs from state/province#seqs from country#seqs from continent
L5#CTT-TTH69-,V70-,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,D614GBelgium_Ghent1446239721Europe 1811060
L5#CTT-TTT19R,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614GBelgium_Ghent2446239721Europe 1811060
L5#CTT-TTT19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614GBelgium_Ghent6446239721Europe 1811060
L5#CTT-TTT19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,Q677H,P681R,D950N,D614GBelgium_Ghent1446239721Europe 1811060
L5#CTT-TTH69-,V70-,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,D614GBelgium_Luxembourg162239721Europe 1811060
L5#CTT-TTE484K,V1176F,D614GBrazil_Minas-Gerais_Desterro-do-Melo1269239661South-America 67618
L5#CTT-TTE484K,V1176F,D614GBrazil_Rio-Grande-do-Sul_Candelaria12179839661South-America 67618
L5#CTT-TTE484K,V1176F,D614GBrazil_Santa-Catarina_Florianopolis120693139661South-America 67618
L5#CTT-TTT95I,Y144X,Y145N,R346K,E484K,N501Y,P681H,D950N,D614GColombia11890South-America 67618
L5#CTT-TTT95I,Y144X,Y145N,R346K,S477N,E484K,N501Y,P681H,D950N,D614GColombia11890South-America 67618
L5#CTT-TTT19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,P681R,D950N,D614GCzech-Republic_Usti-nad-Labem-Region_Litomerice_Lovosice13526486Europe 1811060
L5#CTT-TTH69-,V70-,D614GDenmark1155577Europe 1811060
L5#CTT-TTH69-,V70-,F490S,N501Y,A570D,P681H,T716I,S982A,D1118H,D614GDenmark1155577Europe 1811060
L5#CTT-TTA222V,A262S,D614GDenmark_Hovedstaden169833155577Europe 1811060
L5#CTT-TTA222V,D614GDenmark_Hovedstaden269833155577Europe 1811060
L5#CTT-TTH69-,V70-,N439K,D614GDenmark_Hovedstaden169833155577Europe 1811060
L5#CTT-TTH69-,V70-,Y144-,E484K,N501Y,A570D,P681H,T716I,S982A,D1118H,D614GDenmark_Hovedstaden169833155577Europe 1811060
L5#CTT-TTH69-,V70-,Y144-,F490S,N501Y,A570D,P681H,T716I,S982A,D1118H,D614GDenmark_Hovedstaden469833155577Europe 1811060
L5#CTT-TTH69-,V70-,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,D614GDenmark_Hovedstaden1669833155577Europe 1811060
L5#CTT-TTH69-,V70-,Y144-,W152R,N501Y,A570D,P681H,T716I,S982A,D1118H,D614GDenmark_Hovedstaden1369833155577Europe 1811060
L5#CTT-TTH69-,V70-,Y144X,W152R,N501Y,A570D,P681H,T716I,S982A,D1118H,D614GDenmark_Hovedstaden169833155577Europe 1811060
L5#CTT-TTL18F,A222V,D614GDenmark_Hovedstaden169833155577Europe 1811060
L5#CTT-TTS477N,D614GDenmark_Hovedstaden369833155577Europe 1811060
L5#CTT-TTA222V,D614GDenmark_Midtjylland729028155577Europe 1811060
L5#CTT-TTH69-,V70-,Y144-,F490S,N501Y,A570D,P681H,T716I,S982A,D1118H,D614GDenmark_Midtjylland1329028155577Europe 1811060
L5#CTT-TTH69-,V70-,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,D614GDenmark_Midtjylland1129028155577Europe 1811060
L5#CTT-TTH69-,V70-,Y144X,N501Y,A570D,P681H,T716I,S982A,D1118H,D614GDenmark_Midtjylland129028155577Europe 1811060
L5#CTT-TTL18F,A222V,D614GDenmark_Midtjylland129028155577Europe 1811060
L5#CTT-TTL18F,Y144-,A222V,D614GDenmark_Midtjylland129028155577Europe 1811060
L5#CTT-TTS477R,D614GDenmark_Midtjylland129028155577Europe 1811060
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L5#CTT-TTH69-,V70-,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,P1162S,D614GGabon_Lambarene590142Africa 20313
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L5#CTT-TTH69-,V70-,Y144-,N501Y,A570D,P681H,T716I,S982A,D1118H,D614GSweden_Uppsala8184499113Europe 1811060
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