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COVID-19 Viral Genome Analysis Pipeline
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XSpike

eXplore the Spike protein sequence in the SARS CoV-2 virus

Last update: Sep 12, 2021
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Global
Variants color key
Evaluating 401327 sequences of length 2071
Sampled from 2021-07-02 to 2021-08-31.
Specified Date Range: (datetime.date(2021, 7, 2), datetime.date(2021, 8, 31))
Highest entropy sites for: Global
  Site Entropy
    95  0.6796
   142  0.5796
   222  0.3206
   681  0.3180
   950  0.2972
   158  0.2849
   156  0.2823
   157  0.2810
   452  0.2744
   478  0.2686
    19  0.2649
   501  0.2213
    70  0.1920
   144  0.1778
   570  0.1534
    69  0.1505
   716  0.1462
  1118  0.1433
   982  0.1420
   484  0.1266
   138  0.1182
  1264  0.1056
   417  0.1026
    18  0.0957
  1027  0.0913
    20  0.0856
    26  0.0851
   655  0.0837
   112  0.0835
  1176  0.0813
   190  0.0794
   289  0.0774
   251  0.0699
   145  0.0618
     5  0.0543
    77  0.0536
  1104  0.0487
   719  0.0439
   250  0.0422
    67  0.0396
    21  0.0392
   850  0.0374
  1074  0.0351
   181  0.0339
   253  0.0332
  1162  0.0322
    29  0.0308
   677  0.0291
   346  0.0281
    27  0.0281


Most highly correlated site-pairs for: Global
               cramerV  mutInfo
   156    157   0.4996   0.2755
   158    156   0.5789   0.2744
   158    157   0.6707   0.2707
   157    478   0.5566   0.2442
   156    478   0.5563   0.2441
   681    478   0.5601   0.2425
   158    478   0.5526   0.2413
   681    157   0.4800   0.2408
   681    156   0.4797   0.2407
   452    478   0.5576   0.2397
   681    158   0.5536   0.2387
   681    452   0.4870   0.2336
   478     19   0.5513   0.2317
   157    452   0.4731   0.2309
   157     19   0.4722   0.2303


   570    982   0.7037   0.1390
   570   1118   0.7002   0.1369
  1118    982   0.6998   0.1370
   716    982   0.6913   0.1348
   417   1176   0.6882   0.0747
  1176    190   0.6879   0.0746
   716   1118   0.6871   0.1327
    69    982   0.6871   0.1334
    70    982   0.6871   0.1334
    20   1176   0.6869   0.0742
    70   1118   0.6865   0.1332
    69   1118   0.6865   0.1332
   655    190   0.6753   0.0729
   138   1176   0.6748   0.0717
   417    655   0.6735   0.0724


Most common patterns for local area, where Local = Global
                                           1111111
             1111111111222223444455666778990011112
 1122222667791344455589255584157807578115582701676
58901679790752824567810201396728410571690027448264
LLTTRPATAHVKTSDGYYEFRGRATPDVRKLTENAHQPTTIDSTNVDPVV  Global     UK  Eu-UK  NAmer   Asia Africa  SAmer  Ocean   Local  Exact  Pct [Context]
                                                    401327 128132 135888 116083  13359    355   5485   2025  401327 <----------- Totals
..R.........I..D..G--.........RK.....R...N........  126894  92846  18880  10083   3458      9    489   1129  126894  99951  78% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--.........RK.....R...N........  104997  18031  46833  39271    457    102    257     46  104997  89193  84% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--.........RK.....R...N........   32589    485  13479  17500    539     51    535      0   32589  26313  80% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--..V......RK.....R...N........   16109   2449   8400   4037    985     12    204     22   16109  12849  79% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I.....G--.........RK.....R...N........   13459    931   7059   4440    319      8     42    660   13459  10639  79% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.........--.....-................YD..HI...A...H...   10789    251   5477   2975   2001      5     45     35   10789   5859  54% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.F.N.S........Y.......S......T..KY.Y.......I....F.    4995      6   1035   1867     10      0   2077      0    4995   2839  56% [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
..R..........L.D..G--.........RK.....R...N........    4278      3     20   4245      4      0      4      2    4278   3404  79% [T19R,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--..V......RK.....R...N........    4210    132   1831   1591    653      1      1      1    4210   3231  76% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R............D..G--..V...I..RK.....R...N........    3581      3      2   3569      4      0      3      0    3581   3220  89% [T19R,G142D,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..................................................    3153      1   3084     58      1      2      5      2    3153   2928  92% [D614G] G-clade
..R............D..G--.........RK.....R...N.......L    2888     14    217     89   2557      0      0     11    2888   2602  90% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
..R...............G--.........RK.....R............    2812      4   1007   1497     47      3    254      0    2812   2132  75% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
..R............D..G--....L....RK.....R...N........    2339    687   1522     87     24      0     19      0    2339   1546  66% [T19R,G142D,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R........T...D..G--.........RK.....R...N........    2188     11    306   1863      5      2      1      0    2188   1662  75% [T19R,K77T,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D.HG--..V......RK.....R...N........    2152   2125     26      0      0      0      0      1    2152   1876  87% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I.HD..G--.........RK.....R...N........    1971   1777     78    116      0      0      0      0    1971   1323  67% [T19R,T95I,D138H,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R..........L....G--.........RK.....R...N........    1931      0     14   1916      1      0      0      0    1931   1603  83% [T19R,S112L,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--..V......RK.....R...N.......L    1829    126     99   1587     15      2      0      0    1829   1197  65% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+A222V
..R.........I..D..G--.........RK.....R.I.N........    1825     35   1731     34      2      0     20      3    1825   1639  89% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T719I,D950N] B.1.617.2=Delta
..R...............G--..V...I..RK.....R...N........    1656      0      2   1651      2      0      1      0    1656   1478  89% [T19R,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I..D..G--.........RK.....R...N...L....    1615    154    192   1249     18      0      2      0    1615    895  55% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] B.1.617.2=Delta
..R...............G--....L....RK.....R...N........    1518     29   1467     13      7      1      1      0    1518   1288  84% [T19R,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--..V......RK.....R...N..S....L    1304     14     24   1251      3      0     12      0    1304   1127  86% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,N1074S,V1264L] Delta+A222V
..R.T..........D..G--..V......RK.....R...N........    1274     32   1230      2      2      0      8      0    1274   1104  86% [T19R,R21T,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I..D..G--.........RK.....R..LN........    1205     10   1160     27      8      0      0      0    1205    899  74% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] B.1.617.2=Delta
..R.........I.....G--.........RK.....R...N...L....    1088     27    139    905      5      0     12      0    1088    568  52% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] B.1.617.2=Delta
............I...SN..........K...KY...H...N........    1059      2     64    877      1      0    115      0    1059    613  57% [T95I,+143T,Y144S,Y145N,R346K,E484K,N501Y,D614G,P681H,D950N] B.1.621
..R........T......G--.........RK.....R...N........    1026      2    118    903      3      0      0      0    1026    812  79% [T19R,K77T,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D..G--.........RK.....R...N.....S..    1006    969     20     14      3      0      0      0    1006    906  90% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162S] B.1.617.2=Delta
..R.........I.....G--.........RK.....R.I.N........     964     15    938     11      0      0      0      0     964    889  92% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T719I,D950N] B.1.617.2=Delta
..R....A.......D..G--...I.....RK.....R...N........     938     33    874     23      5      0      0      3     938    442  47% [T19R,T29A,G142D,E156G,F157-,R158-,T250I,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--..V......RK.....R...N.......L     937      0     28    858     48      0      3      0     937    673  71% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+A222V
F.R.........I..D..G--.........RK.....R...N........     887    587    114     95     91      0      0      0     887    656  73% [L5F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I.....G--.........RK.....R............     843     43    343    423     18      1      9      6     843    646  76% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
.................................Y................     795      0    795      0      0      0      0      0     795    756  95% [N501Y,D614G] G-clade
..R.......F.I..D..G--.........RK.....R...N........     780    725     52      1      2      0      0      0     780    618  79% [T19R,V70F,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
..R.........I..D..G--.........RK....HR...N........     749    155    497     78     13      1      5      0     749    503  67% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,D950N] B.1.617.2=Delta
F.R............D..G--.........RK.....R...N........     747     96    261    378     10      0      2      0     747    611  81% [L5F,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--..V......RK.....R...N..S....L     732      5     20    701      3      0      3      0     732    617  84% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,N1074S,V1264L] Delta+A222V
..R.......I....D..G--.........RK.....R...N........     569      1      3    565      0      0      0      0     569    355  62% [T19R,V70I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
..R...S........D..G--.........RK.....R...N........     540     66    445     18      1      0     10      0     540    478  88% [T19R,A27S,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--..V......RK.....R............     537      0    143    191    203      0      0      0     537    419  78% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R] 
..R.............................K........N........     502      0    502      0      0      0      0      0     502    498  99% [T19R,E484K,D614G,D950N] 
................................K..........I......     496      0     40      1    455      0      0      0     496    442  89% [I210T,N440K,E484K,D614G,D936N,S939F,T1027I] B.1.619
.F.N.S........Y.......S......T..KY.Y.H.....I....F.     480      0     91     73      1      0    315      0     480    370  77% [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,P681H,T1027I,V1176F] P.1=Gamma
..R............D..G--V........RK.....R...N........     478     33    334    110      1      0      0      0     478    376  78% [T19R,G142D,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.FR.........I..D..G--.........RK.....R...N........     463    431     20     12      0      0      0      0     463    301  65% [L18F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.....V......D..G--..V......RK.....R...N........     455      4    367     28      2      0     54      0     455    436  95% [T19R,A67V,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I.....G--.........RK....HR...N........     447      7    408     21      2      0      9      0     447    322  72% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,D950N] B.1.617.2=Delta
..R.......I.......G--.........RK.....R...N........     446      0      3    442      1      0      0      0     446    341  76% [T19R,V70I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
..R............D..G--..V..A...RK.....R...N........     444      3    435      3      3      0      0      0     444    337  75% [T19R,G142D,E156G,F157-,R158-,A222V,D253A,L452R,T478K,D614G,P681R,D950N,D979E] Delta+A222V
..R.....V......D..G--.........RK.....R...N........     421    391      7     23      0      0      0      0     421    373  88% [T19R,T22I,A67V,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.......F....D..G--..V.....NRK.....R...N........     409      0      1    407      0      0      1      0     409    367  89% [T19R,V70F,G142D,E156G,F157-,R158-,A222V,K417N,L452R,T478K,D614G,P681R,D950N] Delta-AY.2
..R....A..........G--...I.....RK.....R...N........     406     15    370     14      7      0      0      0     406    162  39% [T19R,T29A,E156G,F157-,R158-,T250I,T299I,L452R,T478K,Q613H,D614G,P681R,D950N] B.1.617.2=Delta
........................---...Q...................     396      0     41     80      3      1    271      0     396    254  64% [G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,T859N] C.37=Lambda
..R.....V...I..D..G--.........RK.....R...N........     396    386      3      6      1      0      0      0     396    358  90% [T19R,A67V,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...S.....I..D..G--.........RK.....R...N........     384     24     17    343      0      0      0      0     384    336  87% [T19R,A27S,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I.....G--.........RK.....R..LN........     376      0    346      7     23      0      0      0     376    204  54% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] B.1.617.2=Delta
..R...............G--V........RK.....R...N........     358      9    317     21      8      0      3      0     358    246  68% [T19R,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
F.R...............G--.........RK.....R...N........     348      3    139    190     13      0      3      0     348    258  74% [L5F,T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--.........RK.....R............     340      0    259     60     14      2      5      0     340    284  83% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
..R...........................RK.....R...N........     337      1    124     44    167      0      1      0     337    241  71% [T19R,L452R,T478K,D614G,P681R,D950N] 
..R............D..G--.........RK.....R..LN........     326      0    326      0      0      0      0      0     326    303  92% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] B.1.617.2=Delta
.R..........I.......S................H.....I......     323      0      0    323      0      0      0      0     323    190  58% [L18R,T95I,R158S,N440K,D614G,P681H,A688V,S735A,T1027I] 
F........--.....-................YD..HI...A...H...     313      7    160    130     15      0      0      1     313    130  41% [L5F,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R...............G--.........RK..S..R...N........     310      1    307      1      1      0      0      0     310    275  88% [T19R,E156G,F157-,R158-,L452R,T478K,A570S,D614G,P681R,D950N] B.1.617.2=Delta
..R.....S......D..G--.........RK.....R...N........     307     17    280      9      0      0      1      0     307    276  89% [T19R,A67S,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.I.......I..D..G--.........RK.....R...N........     306    298      0      5      3      0      0      0     306    267  87% [T19R,R21I,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.T.............G--..V......RK.....R...N........     296      9    286      0      1      0      0      0     296    260  87% [T19R,R21T,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I..D..G--E........RK.....R...N........     280    274      5      0      1      0      0      0     280    261  93% [T19R,T95I,G142D,E156G,F157-,R158-,G181E,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--..........K.....R...N........     267      0    245     18      4      0      0      0     267    256  95% [T19R,E156G,F157-,R158-,T478K,D614G,P681R,D950N] 
..R............D..G--.........RK.....RI..N........     242     71      9     22      1      0    139      0     242    190  78% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T716I,D950N] B.1.617.2=Delta
..R..............................Y................     241      0    241      0      0      0      0      0     241    241 100% [T19R,N501Y,D614G] 
..R.........I.....G--.........RK.....R.......L....     236      0      4    226      0      0      6      0     236     44  18% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,V1104L] 
..R..............................Y.......N........     222      0    222      0      0      0      0      0     222    222 100% [T19R,N501Y,D614G,D950N] 
..............................R......R............     218      0    218      0      0      0      0      0     218    218 100% [L452R,D614G,P681R] 
..R............D..--..........RK.....R...N........     217      0    217      0      0      0      0      0     217    212  97% [T19R,G142D,S155R,E156-,F157-,L452R,T478K,D614G,P681R,D950N] 
..R...............G--.........RK.....R...N.......L     214      1    118     18     75      0      0      2     214    173  80% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
..R.........I..D..G--.....G...RK.....R...N........     204    196      4      1      3      0      0      0     204    177  86% [T19R,T95I,G142D,E156G,F157-,R158-,D253G,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--.........RK...Y.R...N........     202     10    162     30      0      0      0      0     202    124  61% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,H655Y,P681R,P792S,D950N] B.1.617.2=Delta
..R.........I..D..G--.........RK.....R...N.......L     202    188      8      2      4      0      0      0     202    173  85% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
..R...............G--.........RK..S..R............     196      0    195      0      1      0      0      0     196    182  92% [T19R,E156G,F157-,R158-,L452R,T478K,A570S,D614G,P681R] 
............I...-...............K....H............     194      2    126     24      1     41      0      0     194    143  73% [T95I,Y144-,E484K,D614G,P681H,D796H] B.1.1.318
..R.........I..D..G--V........RK.....R...N........     194    161     19      1     12      0      0      1     194    166  85% [T19R,T95I,G142D,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.........--...H.-................YD..HI...A...H...     194      7    129     53      4      1      0      0     194     78  40% [H69-,V70-,D138H,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.........I..D..G--........NRK.....R...N........     190     42     15    127      4      0      0      2     190    130  68% [T19R,T95I,G142D,E156G,F157-,R158-,W258L,K417N,L452R,T478K,D614G,P681R,D950N] Delta-AY.1
............I...SN..........KN..KY...H...N........     188     17      7    159      1      0      4      0     188    170  90% [T95I,+143T,Y144S,Y145N,R346K,K417N,E484K,N501Y,D614G,P681H,D950N] B.1.621
..R...S...........G--.........RK.....R...N........     187     13    163      8      2      0      1      0     187    154  82% [T19R,A27S,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
F.R.........I.....G--.........RK.....R...N........     187      3     93     82      9      0      0      0     187    131  70% [L5F,T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R..S......I..D..G--.........RK.....R...N........     184    147     32      4      1      0      0      0     184    106  57% [T19R,P26S,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D..G--...N.....RK.....R...N........     184    183      1      0      0      0      0      0     184    166  90% [T19R,T95I,G142D,E156G,F157-,R158-,T250N,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..............................R...................     182      0    177      4      0      0      1      0     182    173  95% [L452R,D614G] 
.........--.....-...............KYD..HI...A...H...     182      1    113      7     59      0      2      0     182    124  68% [H69-,V70-,Y144-,E484K,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+E484K
..R............D..G-..........RK.....R...N........     172      0    172      0      0      0      0      0     172    171  99% [T19R,G142D,E156G,F157-,L452R,T478K,D614G,P681R,D950N] 
..R.......F.......G--..V.....NRK.....R...N........     166      0      0    166      0      0      0      0     166    142  85% [T19R,V70F,E156G,F157-,R158-,A222V,K417N,L452R,T478K,D614G,P681R,D950N] Delta-AY.2
..R...............G--..V...I..RK.....R............     151      0      0    151      0      0      0      0     151    133  88% [T19R,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R] 
..R...............G--..V..A...RK.....R...N........     150      1    146      2      1      0      0      0     150    125  83% [T19R,E156G,F157-,R158-,A222V,D253A,L452R,T478K,D614G,P681R,D950N,D979E] Delta+A222V
........V--.....-................YD..HI...A...H...     150      1    148      0      1      0      0      0     150    132  88% [A67V,H69-,V70-,S98F,Y144-,N501Y,A570D,D614G,P681H,T716I,D936Y,S982A,D1118H] B.1.1.7=Alpha
..R...............G--.........RK.....R..LN........     146      0    146      0      0      0      0      0     146    125  85% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] B.1.617.2=Delta
..R..........L....G--.........RK.....R............     141      0      2    138      1      0      0      0     141    113  80% [T19R,S112L,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
..R...S.....I.....G--.........RK.....R...N........     140      0      4    136      0      0      0      0     140    126  90% [T19R,A27S,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.................................Y.......N........     139      0    139      0      0      0      0      0     139    137  98% [N501Y,D614G,D950N] 
...............Y-.............R...................     138      0      2    133      0      0      3      0     138     59  42% [L141-,G142Y,V143-,Y144-,+214AAG,D215Y,L452R,D614G] 
..R.........I..D..G--.........RK.....RI..N........     134    132      0      2      0      0      0      0     134    109  81% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T716I,D950N] B.1.617.2=Delta
..............................RK..................     133      0    132      0      1      0      0      0     133    131  98% [L452R,T478K,D614G] 
..R............D..G--.........RK.....R...N.....L..     131     22     36     72      0      0      1      0     131    114  87% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162L] B.1.617.2=Delta
..R.........I..D..G--.........RK...Y.R...N........     129     89      0     37      3      0      0      0     129    109  84% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,H655Y,P681R,D950N] B.1.617.2=Delta
F...........I.............G.....K.................     125      0      1     85      0      0     39      0     125     73  58% [L5F,T95I,D253G,E484K,D614G,A701V] B.1.526=Iota
................-..S..........R..........H........     118      0      0    118      0      0      0      0     118     68  57% [D80G,Y144-,F157S,L452R,D614G,T859N,D950H] B.1.526.1
..R............D..G--.........RK....HR...N........     114      3     61     47      3      0      0      0     114     72  63% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,D950N] B.1.617.2=Delta
..R...........................RK.....R............     113      0     26      3     82      2      0      0     113     42  37% [T19R,L452R,T478K,D614G,P681R] 
.F...........................N..KY................     112      0     58      6      9     39      0      0     112     70  62% [L18F,D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,A701V] B.1.351=Beta
..R........T......G--.........RK.....R............     109      0      5    104      0      0      0      0     109     83  76% [T19R,K77T,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
..R...............G--.........RK.Y...R...N........     105      0    105      0      0      0      0      0     105    103  98% [T19R,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--..........K.....R...N........     105      0     92     13      0      0      0      0     105     80  76% [T19R,G142D,E156G,F157-,R158-,T478K,D614G,P681R,D950N] 
F.R............D..G--..V......RK.....R...N........     105     21     20     49     15      0      0      0     105     61  58% [L5F,T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.I..........D..G--.........RK.....R...N........     105      5     68     30      1      1      0      0     105     94  89% [T19R,R21I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R........T...D..G--.........RKQ....R...N........     104      0      1    103      0      0      0      0     104     91  87% [T19R,K77T,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D..G--.........RK.....R............     104      2     89      7      6      0      0      0     104     81  77% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
................................KY................     102      0    102      0      0      0      0      0     102     91  89% [E484K,N501Y,D614G] 
..R....I....I..D..G--.........RK.....R...N........     102     91     10      1      0      0      0      0     102     89  87% [T19R,T29I,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R..............................Y...R...N........     101      0    101      0      0      0      0      0     101    101 100% [T19R,N501Y,D614G,P681R,D950N] 
..R...............G--....L....RK.....R............      96      0     92      3      0      0      1      0      96     83  86% [T19R,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R] 
..R.........I..D..G--......L..RK.....R...N........      95     94      0      0      1      0      0      0      95     89  93% [T19R,T95I,G142D,E156G,F157-,R158-,V289L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D-.G--.........RK.....R...N........      93     40     22     30      0      1      0      0      93     63  67% [T19R,G142D,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R......--.......G--.........RK.....R...N........      92      5     50     37      0      0      0      0      92     65  70% [T19R,H69-,V70-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
..R............D..G--..V......RK.....R...N.....S..      89     20     43     25      1      0      0      0      89     67  75% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,P1162S] Delta+A222V
..R............D..G--..V......RK.....R............      88      3     25      7     53      0      0      0      88     70  79% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R] 
..R.........I..D..G--.........RK.....R...N.I......      88     71     10      7      0      0      0      0      88     35  39% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,T1027I] B.1.617.2=Delta
..R.I.............G--.........RK.....R...N........      88      0     80      6      2      0      0      0      88     74  84% [T19R,R21I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
...............D..G--.........RK.....R...N........      83      5     36     42      0      0      0      0      83     72  86% [G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
..R.........I..D..G--..V......RK.....R...N........      83     19     52      4      8      0      0      0      83     37  44% [T19R,T95I,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R...............................................      82      0     80      2      0      0      0      0      82     71  86% [T19R,D614G] 
..R.....S...I..D..G--.........RK.....R...N........      81     59     18      2      2      0      0      0      81     75  92% [T19R,A67S,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.........--.....-................YD.HHI...A...H...      79      1     62     11      5      0      0      0      79     48  60% [H69-,V70-,Y144-,N501Y,A570D,D614G,Q677H,P681H,V687L,T716I,S982A,D1118H] B.1.1.7=Alpha
..R............D..G--..V.L....RK.....R...N........      77      0     63      0     14      0      0      0      77     69  89% [T19R,G142D,E156G,F157-,R158-,A222V,P251L,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I..D.HG--..V......RK.....R...N.......L      77     77      0      0      0      0      0      0      77     73  94% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+A222V
..R......................................N........      75      0     75      0      0      0      0      0      75     74  98% [T19R,D614G,D950N] 
..R............D..............RK.....R...N........      74      0     43      9     22      0      0      0      74     64  86% [T19R,G142D,L452R,T478K,D614G,P681R,D950N] 
..R.........I..D-.G--.........RK.....R...N........      74     18     53      3      0      0      0      0      74     67  90% [T19R,T95I,G142D,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D..G--.........RK.....R...N.....L..      73     63      3      7      0      0      0      0      73     47  64% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162L] B.1.617.2=Delta
.....S...--.....-...............K....H.....I..H...      73      0      3      0     69      1      0      0      73     48  65% [P26S,H69-,V70-,V126A,Y144-,L242-,A243-,L244-,H245Y,S477N,E484K,D614G,P681H,T1027I,D1118H] B.1.620
F...........I.............G.......................      70      0      0     69      0      0      1      0      70     27  38% [L5F,T95I,D253G,S477N,D614G,A701V] B.1.526=Iota
..R.........I.YD..G--.........RK.....R...N........      70     20     48      2      0      0      0      0      70     62  88% [T19R,T95I,D138Y,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D..G--.........RK.....R...N......F.      69     64      2      2      1      0      0      0      69     67  97% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1176F] B.1.617.2=Delta
................................K.................      68      0     63      1      4      0      0      0      68     52  76% [E484K,D614G] 
F.R.........I.HD..G--.........RK.....R...N........      68     68      0      0      0      0      0      0      68     38  55% [L5F,T19R,T95I,D138H,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I.....G--.........RK.....R.I..........      68      0     67      1      0      0      0      0      68     62  91% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T719I] 
..RI...........D..G--.........RK.....R...N........      67      3     31     26      7      0      0      0      67     48  71% [T19R,T20I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D.HG--.........RK.....R...N........      67     65      0      2      0      0      0      0      67     66  98% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--.........RK..S..R...N........      66     32     31      1      2      0      0      0      66     32  48% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,A570S,D614G,P681R,D950N] B.1.617.2=Delta
.............................N..KY................      66      0     37      0      0     29      0      0      66     24  36% [D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,A701V] B.1.351=Beta
................-..S..........R......H...H........      65      0      0     65      0      0      0      0      65     56  86% [D80G,Y144-,F157S,L452R,D614G,P681H,T859N,D950H] B.1.526.1
..R............D..G--.........RK.....R...N...L....      64      5     33     13     12      1      0      0      64     46  71% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] B.1.617.2=Delta
..R........T......G--.........RKQ....R...N........      63      0      0     63      0      0      0      0      63     49  77% [T19R,K77T,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
..............................RK.....R............      62      0     61      1      0      0      0      0      62     61  98% [L452R,T478K,D614G,P681R] 
.F.N.S........Y.......S......T..KY.Y.R.....I....F.      62      1      5      0      0      0     56      0      62     40  64% [L18F,T20N,P26S,D138Y,R190S,K417T,T470N,E484K,N501Y,D614G,H655Y,P681R,T1027I,V1176F,C1235F] P.1=Gamma
..R...............G--.........RK.....R...N...L....      61      1     36     19      4      1      0      0      61     47  77% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] B.1.617.2=Delta
.FR............D..G--.........RK.....R...N........      61      8     16     36      0      0      1      0      61     38  62% [L18F,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.........--.................S.R.....H.............      59      0     33     25      1      0      0      0      59     31  52% [S12F,H69-,V70-,W152R,R346S,L452R,D614G,Q677H,A899S] C.36
..R.........I.....G--.........RK.....R...N.....A..      59      0      0      0      0      0      0     59      59     53  89% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162A] B.1.617.2=Delta
..R............D..G--..VS.....RK.....R...N........      58      4     40      8      2      2      0      2      58     52  89% [T19R,G142D,E156G,F157-,R158-,A222V,T250S,L452R,T478K,D614G,P681R,D950N] Delta+A222V
.........--...H.-....V...........YD..HI...A...H...      58      2     56      0      0      0      0      0      58     54  93% [H69-,V70-,S98F,D138H,Y144-,G181V,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..RI........I..D..G--.........RK.....R...N........      57     23     28      4      2      0      0      0      57     51  89% [T19R,T20I,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.F.N.S................S......T..KY.Y.......I....F.      57      0     16     17      0      0     24      0      57     31  54% [L18F,T20N,P26S,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
.....................................R............      56      0     30      0     25      0      1      0      56     30  53% [D614G,P681R] Near-Furin
....I...................---...Q...................      54      1     53      0      0      0      0      0      54     52  96% [R21I,G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,T572I,D614G,Q675H,T859N] C.37=Lambda
..R............D..G--..S......RK.....R...N........      54      1      4     49      0      0      0      0      54     40  74% [T19R,G142D,E156G,F157-,R158-,A222S,L452R,T478K,D614G,E661D,P681R,D950N] 
..R...............G--..V......RK.....R...........L      54      0      0     49      5      0      0      0      54     38  70% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,V1264L] 
..R...............G--................R...N........      53      0     17     35      1      0      0      0      53     42  79% [T19R,E156G,F157-,R158-,D614G,P681R,D950N] 
F.R............D..G--..V...I..RK.....R...N........      53      0      0     53      0      0      0      0      53     50  94% [L5F,T19R,G142D,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R,D950N] Delta+A222V
............I...SN..........K...KY...H............      52      0      1     46      0      0      5      0      52     29  55% [T95I,+143T,Y144S,Y145N,R346K,E484K,N501Y,D614G,P681H] 
..R......--.....-.G--.........RK.....R...N........      51      0     14     37      0      0      0      0      51     48  94% [T19R,H69-,V70-,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
..R......Y..I..D..G--.........RK.....R...N........      50     31     18      1      0      0      0      0      50     38  76% [T19R,H69Y,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.........--.I...-................YD..HI...A...H...      49      0     35     10      4      0      0      0      49     40  81% [H69-,V70-,T95I,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
...............................K.....H............      48      0      2     45      1      0      0      0      48     33  68% [T478K,D614G,P681H,T732A] B.1.1.519
..R............D..G--R........RK.....R...N........      48      1      2     44      1      0      0      0      48     41  85% [T19R,G142D,E156G,F157-,R158-,G181R,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D..G--.........RK.....R..VN........      48     48      0      0      0      0      0      0      48     45  93% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850V,D950N] B.1.617.2=Delta
..R.......G.I..D..G--.........RK.....R...N........      48     47      1      0      0      0      0      0      48     40  83% [T19R,V70G,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
.........--.....-................YD..HI...A.......      48      0     45      3      0      0      0      0      48     42  87% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,A701V,T716I,S982A] 
............I..D..G--.........R......R............      47      0     47      0      0      0      0      0      47     43  91% [T95I,G142D,E156G,F157-,R158-,L452R,D614G,P681R] 
.........--.....-................YD...I...A...H...      47      0     46      1      0      0      0      0      47     46  97% [H69-,V70-,Y144-,N501Y,A570D,D614G,T716I,S982A,D1118H] 
........D--.....-................YD..HI...A...H...      47      0      0     47      0      0      0      0      47     46  97% [A67D,H69-,V70-,Y144-,F490S,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+F490S
..R.........I.................RK.....R............      46      0      7      2     37      0      0      0      46     16  34% [T19R,T95I,L452R,T478K,D614G,P681R] 
..................G--.........RK.....R...N........      45      0     24     19      0      1      1      0      45     36  80% [E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
..R...............G--.........RK.....R...N.....L..      45      0     14     30      1      0      0      0      45     33  73% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162L] B.1.617.2=Delta
..R.........I.....G--........NRK.....R...N........      45      2      6     37      0      0      0      0      45     36  80% [T19R,T95I,E156G,F157-,R158-,W258L,K417N,L452R,T478K,D614G,P681R,D950N] Delta-AY.1
.F...S........Y.......S......T..KY.Y.......I....F.      45      0      1     30      0      0     14      0      45     34  75% [L18F,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] 
.........--.....-................YD..HI...A...HS..      44      1     34      7      2      0      0      0      44     25  56% [H69-,V70-,I100T,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,P1162S] B.1.1.7=Alpha
.........................................N........      43      0     43      0      0      0      0      0      43     41  95% [D614G,D950N] 
..R............D..G--.........RK.....R...N......F.      43      2     38      3      0      0      0      0      43     17  39% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,Q836E,D950N,V1176F] B.1.617.2=Delta
..R.........I...-.G--.........RK.....R...N........      43      0     43      0      0      0      0      0      43     37  86% [T19R,T95I,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I.................RK.....R...N........      43      0     31      9      3      0      0      0      43     38  88% [T19R,T95I,L452R,T478K,D614G,P681R,D950N] 
..R.........I.....G--..V......RK.....R...N........      42      2     15      8     17      0      0      0      42     28  66% [T19R,T95I,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R...............G--..V......RK.....R......S.....      42      0      0     42      0      0      0      0      42     35  83% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,N1074S] 
..RA...........D..G--..V...I..RK.....R...N........      42      0      0     42      0      0      0      0      42     41  97% [T19R,T20A,G142D,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R....A....I.HD..G--.........RK.....R...N........      42     42      0      0      0      0      0      0      42     41  97% [T19R,T29A,T95I,D138H,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D..G--..........K.....R...N........      41      3     37      1      0      0      0      0      41     39  95% [T19R,T95I,G142D,E156G,F157-,R158-,T478K,D614G,P681R,D950N] 
..R...............G--.........RK....HR...N........      41      5     16     19      1      0      0      0      41     27  65% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,D950N] B.1.617.2=Delta
..R....I.......D..G--.........RK.....R...N........      41      0     11     29      0      0      1      0      41     28  68% [T19R,T29I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
FF.N.S........Y.......S......T..KY.Y.......I....F.      41      0      0     10      0      0     31      0      41     29  70% [L5F,L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
........V--.....-............R..KYD..HI...A...H...      41      0      0     41      0      0      0      0      41     21  51% [A67V,H69-,V70-,Y144-,K417R,E484K,N501Y,A570D,D614G,P681H,A701V,T716I,S982A,D1118H,K1191N] Alpha+E484K
...............D..G--.........R......R............      40      0     40      0      0      0      0      0      40     26  65% [G142D,E156G,F157-,R158-,L452R,D614G,P681R] 
.R..........I.......S.........M......H.....I......      40      0      0     40      0      0      0      0      40     12  30% [L18R,T95I,R158S,L176F,N440K,L452M,D614G,P681H,A688V,S735A,T1027I] 
..R.......F....D..G--.........RK.....R...N........      40      1     20     19      0      0      0      0      40     32  80% [T19R,V70F,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
F.R............D..G--..V......RK.....R...N..S....L      40      0      0     40      0      0      0      0      40     29  72% [L5F,T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,N1074S,V1264L] Delta+A222V
..R.........I.....G--.........RK....HR............      40      0     26      3      1      0     10      0      40     29  72% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R] 
..R.....S.........G--.........RK.....R...N........      40      4     26     10      0      0      0      0      40     31  77% [T19R,A67S,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.....S...I..D..G--.........RK.....R...N.....S..      40     40      0      0      0      0      0      0      40     39  97% [T19R,A67S,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162S] B.1.617.2=Delta
..R...............G--..V.L....RK.....R...N........      39      0     37      1      1      0      0      0      39     36  92% [T19R,E156G,F157-,R158-,A222V,P251L,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R...V...........G--.........RK.....R...N........      38      0     32      6      0      0      0      0      38     33  86% [T19R,A27V,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...V...........G--.........RK.....R............      38      0     37      1      0      0      0      0      38     23  60% [T19R,A27V,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
F.R.........I..D.HG--..V......RK.....R...N........      38     38      0      0      0      0      0      0      38     37  97% [L5F,T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R......--.....-.............RK.....R...N........      38      0     25     13      0      0      0      0      38     26  68% [T19R,H69-,V70-,Y144-,L452R,T478K,D614G,P681R,D950N] 
.........--.....-....A...........YD..HI...A...H...      38      0      0     38      0      0      0      0      38     33  86% [H69-,V70-,Y144-,G181A,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.........I..D..G--.........RK.....H...N........      35      6     28      0      1      0      0      0      35     31  88% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681H,D950N] 
..R.........I.AD..G--.........RK.....R...N........      35     35      0      0      0      0      0      0      35     27  77% [T19R,T95I,D138A,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.......I...........S............K..Y.H............      35      0      5     30      0      0      0      0      35     30  85% [T29I,F32L,M153T,F157S,G252V,S477N,E484K,D614G,H655Y,P681H,D936H,D1260H] 
..R............D..G--.........RK.....R...N.....S..      34      3      5     24      2      0      0      0      34     25  73% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162S] B.1.617.2=Delta
..R............D..G--..V...L..RK.....R...N........      34      2     22      0     10      0      0      0      34     29  85% [T19R,G142D,E156G,F157-,R158-,A222V,V289L,L452R,T478K,D614G,P681R,D950N] Delta+A222V
F.R............D..G--..V......RK.....R...N.......L      34      0      2     32      0      0      0      0      34     23  67% [L5F,T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+A222V
F.R............D..G--..V......RK.....R...N......FL      34      0      0     34      0      0      0      0      34     31  91% [L5F,T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,P809S,D950N,V1176F,V1264L] Delta+A222V
..R........TI.....G--.........RK.....R...N........      34      0     34      0      0      0      0      0      34     25  73% [Q14H,T19R,K77T,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.......I.......G--.........RK.....R............      34      0      0     34      0      0      0      0      34     26  76% [T19R,V70I,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
..R.........I.....G--.........RK.Y...R..LN........      34      0     34      0      0      0      0      0      34     33  97% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681R,I850L,D950N] B.1.617.2=Delta
..R...............G--..S......RK.....R...N........      33      0      5     28      0      0      0      0      33     20  60% [T19R,E156G,F157-,R158-,A222S,L452R,T478K,D614G,E661D,P681R,D950N] 
..R.T.......I..D..G--.........RK.....R...N........      33     27      2      1      3      0      0      0      33     16  48% [T19R,R21T,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
F.R...............G--..V......RK.....R...N........      33      0      3     20     10      0      0      0      33     15  45% [L5F,T19R,E156G,F157-,R158-,A222V,V367L,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I..D..G--.........RK.....R...N.....A..      33      0      0      0      0      0      0     33      33     33 100% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162A] B.1.617.2=Delta
.........--.....-................YD..HV...A...H...      33      1     27      4      1      0      0      0      33     23  69% [H69-,V70-,Y144-,N501Y,A570D,D614G,T632I,P681H,T716V,G932V,S982A,D1118H] 
..R.........I..D..G--...I.....RK.....R...N........      32     28      0      4      0      0      0      0      32     22  68% [T19R,T95I,G142D,E156G,F157-,R158-,T250I,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...........Y...G--.........RK.....R...N........      32      0      5     17      0      0     10      0      32     28  87% [T19R,D138Y,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..............................RK.....R...N........      31      0      7     24      0      0      0      0      31     20  64% [L452R,T478K,D614G,P681R,D950N] 
..R..................................R...N........      31      0     29      2      0      0      0      0      31     25  80% [T19R,D614G,P681R,D950N] 
........V--.....-...............K...H.............      31      0     27      3      1      0      0      0      31     22  70% [Q52R,A67V,H69-,V70-,Y144-,E484K,D614G,Q677H,F888L] B.1.525=Eta
..R..............................Y...R............      31      0     31      0      0      0      0      0      31     31 100% [T19R,N501Y,D614G,P681R] 
F...........I...SN..........K...KY...H...N........      30      0      0     24      0      0      6      0      30     10  33% [L5F,T95I,+143T,Y144S,Y145N,R346K,E484K,N501Y,D614G,P681H,D950N] B.1.621
..R...V.....I..D..G--.........RK.....R...N........      30     19      9      2      0      0      0      0      30     26  86% [T19R,A27V,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
...............D..G--.........RK.Y...R...N........      30      0     30      0      0      0      0      0      30     30 100% [G142D,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681R,D950N] 
..R............D..G--..........K.....R..LN........      30      0     30      0      0      0      0      0      30     27  90% [T19R,G142D,E156G,F157-,R158-,T478K,D614G,P681R,I850L,D950N] 
..R.........I..D..G--.........RK.Y...H...N........      30      0     30      0      0      0      0      0      30     30 100% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681H,D950N] 
..RI...........D..G--..V......RK.....R...N........      29      0     28      1      0      0      0      0      29     28  96% [T19R,T20I,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,S1252F] Delta+A222V
..R.........I..D..G--.........RK.Y...R..LN........      29      0     29      0      0      0      0      0      29     29 100% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681R,I850L,D950N] B.1.617.2=Delta
..R.............-.G--.........RK.....R...N........      29      0     14     14      1      0      0      0      29     17  58% [T19R,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R..L......I..D..G--.........RK.....R...N........      29     23      5      0      1      0      0      0      29     27  93% [T19R,P26L,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.....................................R...N........      29      0     26      3      0      0      0      0      29     19  65% [V130A,D614G,P681R,D950N] 
............I...............K...KY...H...N........      28      0      2     26      0      0      0      0      28     16  57% [T95I,R346K,E484K,N501Y,D614G,P681H,D950N] 
..R....I..........G--.........RK.....R...N........      28      0      5     22      0      0      1      0      28     25  89% [T19R,T29I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
F.R...S........D..G--.........RK.....R...N........      28      0     28      0      0      0      0      0      28     16  57% [L5F,T19R,A27S,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--...I.....RK.........N........      28      0     28      0      0      0      0      0      28     28 100% [T19R,G142D,E156G,F157-,R158-,T250I,L452R,T478K,D614G,D950N] 
..R..................................R............      28      0     28      0      0      0      0      0      28     24  85% [T19R,D614G,P681R] 
..RI..............G--.........RK.....R...N........      27      0      2     25      0      0      0      0      27     19  70% [T19R,T20I,E156G,F157-,R158-,P174S,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I.....G--..........K.....R...N........      27      0     22      3      2      0      0      0      27     25  92% [T19R,T95I,E156G,F157-,R158-,T478K,D614G,P681R,D950N] 
..R...............G--.........RK.....R...........L      27      0     18      4      5      0      0      0      27     23  85% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,V1264L] 
.................................Y...R...N........      27      0     27      0      0      0      0      0      27     27 100% [N501Y,D614G,P681R,D950N] 
...............................K..................      27      0     27      0      0      0      0      0      27     27 100% [T478K,D614G] 
..R...............G--.........RK...Y.R...N........      26      0      3     23      0      0      0      0      26     18  69% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,H655Y,P681R,D950N] B.1.617.2=Delta
..R....................V......RK.....R...N........      26      0      7      3     16      0      0      0      26     18  69% [T19R,A222V,L452R,T478K,D614G,P681R,D950N] 
..R...........................RK.Y...R...N........      26      0     26      0      0      0      0      0      26     20  76% [T19R,L452R,T478K,N501Y,D614G,P681R,D950N] 
F.R...............G--....L....RK.....R...N........      25      0     25      0      0      0      0      0      25     22  88% [L5F,T19R,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.............................N....................      25      0     25      0      0      0      0      0      25     25 100% [K417N,D614G] 
..G.........I..D..G--.........RK.....R...N........      24     23      1      0      0      0      0      0      24     17  70% [T19G,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
..R.....V.........G--..V......RK.....R...N........      24      2     20      2      0      0      0      0      24     14  58% [T19R,A67V,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R............D..G--V........RK.....R...N.......L      24      2     22      0      0      0      0      0      24     22  91% [T19R,G142D,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
..R.........I..D..G--..S......RK.....R...N........      24     13      6      5      0      0      0      0      24     15  62% [T19R,T95I,G142D,E156G,F157-,R158-,A222S,L452R,T478K,D614G,P681R,D950N] 
F.R...............G--.........RK.....R............      24      0      6     17      0      0      1      0      24     19  79% [L5F,T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
..R...............G--..V......RK.....R......S....L      24      0      0     24      0      0      0      0      24     22  91% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,N1074S,V1264L] 
..R.........I..D..G--.........RKQ....R...N........      24     23      1      0      0      0      0      0      24     21  87% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--.........RK.....R.I.N........      24      0     16      8      0      0      0      0      24     23  95% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T719I,D950N] B.1.617.2=Delta
.........--.....-....V...........YD..HI...A...H...      24      0      2     11     11      0      0      0      24     17  70% [H69-,V70-,Y144-,G181V,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.........--.....-................YD..HI...A...H.F.      24      4     15      5      0      0      0      0      24     20  83% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,V1176F] B.1.1.7=Alpha
..R......Y.....D..G--.........RK.....R...N........      23     10      2     11      0      0      0      0      23     16  69% [T19R,H69Y,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--V.V......RK.....R...N........      23      3      6     14      0      0      0      0      23     16  69% [T19R,G142D,E156G,F157-,R158-,G181V,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R..S......I.....G--.........RK.....R...N........      23      1     20      2      0      0      0      0      23     15  65% [T19R,P26S,L54F,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I.....G--.........RK.....R...N.....S..      23      9     13      1      0      0      0      0      23     21  91% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162S] B.1.617.2=Delta
..R.........I.....G--.........RK.....R...N.....L..      22      1      3     18      0      0      0      0      22     19  86% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162L] B.1.617.2=Delta
..R...............G--R........RK.....R...N........      22      0      0     22      0      0      0      0      22     20  90% [T19R,E156G,F157-,R158-,G181R,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
............I..D..G--.........RK.....R...N........      22      9      3     10      0      0      0      0      22     17  77% [T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
..R....A..........G--...I.....RK.....R............      22      0     20      2      0      0      0      0      22     13  59% [T19R,T29A,E156G,F157-,R158-,T250I,L452R,T478K,D614G,P681R] 
..R...............G--..VS.....RK.....R...N........      22      1     13      0      1      7      0      0      22     19  86% [T19R,E156G,F157-,R158-,A222V,T250S,L452R,T478K,D614G,P681R,D950N] Delta+A222V
F.R............D..G--....L....RK.....R...N........      22      4     18      0      0      0      0      0      22     18  81% [L5F,T19R,G142D,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--.........RK.........N........      22      0     11     11      0      0      0      0      22     18  81% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,D950N] 
..R.........I......--.........RK.....R...N........      22      0      0     21      0      0      0      1      22     22 100% [T19R,T95I,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
..R........T..................RK.....R...N........      22      0     21      1      0      0      0      0      22     22 100% [T19R,K77T,L452R,T478K,D614G,P681R,D950N] 
..R...V.......................RK.....R...N........      22      0     22      0      0      0      0      0      22     18  81% [T19R,A27V,L452R,T478K,D614G,P681R,D950N] 
.F.N.S........Y.......S......T..KY.YH......I....F.      22      0      0     11      0      0     11      0      22      8  36% [L18F,T20N,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,Q677H,T1027I,V1176F] P.1=Gamma
.........--.....-......V.........YD..HI...A...H...      22      0      4     15      3      0      0      0      22     11  50% [H69-,V70-,Y144-,M177I,D178H,A222V,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
...I.....--.....-................YD..HI...A...H...      22      0     11      4      7      0      0      0      22     20  90% [T20I,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha+T20I
..R.......F.......G--..V.....NRK.....R............      21      0      0     21      0      0      0      0      21     17  80% [T19R,V70F,E156G,F157-,R158-,A222V,K417N,L452R,T478K,D614G,P681R] 
..R.....S......D..G--..V......RK.....R...N........      21      0     21      0      0      0      0      0      21     21 100% [T19R,A67S,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.......L.I..D..G--.........RK.....R...N........      21      2     19      0      0      0      0      0      21     15  71% [T19R,V70L,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
..R...............G--..V......RK.....R...N..S.....      21      0      1     20      0      0      0      0      21     19  90% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,N1074S] Delta+A222V
..R.........I..D..G--.........RK.Y...R...N........      21     19      1      1      0      0      0      0      21     19  90% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D..............RK.....R...N........      21      0     14      2      5      0      0      0      21     17  80% [T19R,T95I,G142D,L452R,T478K,D614G,P681R,D950N] 
..........................G.....KY................      21      0     21      0      0      0      0      0      21     21 100% [D253G,E484K,N501Y,D614G] 
..R.....V......D..G--..V......RK.....R...N.......L      20      0      0     20      0      0      0      0      20     18  90% [T19R,A67V,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+A222V
.FR.........I.....G--.........RK.....R...N........      20      4      9      4      2      1      0      0      20     16  80% [L18F,T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I.....G--V........RK.....R...N...L....      20      0      4     16      0      0      0      0      20     16  80% [T19R,T95I,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N,V1104L] B.1.617.2=Delta
..R.....V...I.....G--.........RK.....R...N........      20      4      7      8      1      0      0      0      20     16  80% [T19R,A67V,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...V........D..G--.........RK.....R...N........      20      0      6     14      0      0      0      0      20     20 100% [T19R,A27V,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D..G--.........RKQ....R...N...L....      20     16      3      1      0      0      0      0      20     19  95% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N,V1104L] B.1.617.2=Delta
..R.........I..D..G--.......S.RK.....R...N........      20     20      0      0      0      0      0      0      20     20 100% [T19R,T95I,G142D,E156G,F157-,R158-,R346S,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
.........--.....-...........T....YD..HI...A...H...      20      0      0     18      2      0      0      0      20     19  95% [H69-,V70-,Y144-,R346T,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.................................YD..HI...A...H...      20      0      1     18      0      0      1      0      20     11  55% [N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] 
.........--.....-................YD..HI...A..LH...      20      0     20      0      0      0      0      0      20     15  75% [H69-,V70-,Y144-,W152R,N501Y,A570D,D614G,P681H,T716I,S982A,V1104L,D1118H] Alpha+W152R
.................................Y....I...........      20      0     20      0      0      0      0      0      20     20 100% [N501Y,D614G,T716I] 
F.R........T...D..G--.........RKQ....R...N........      19      0      0     19      0      0      0      0      19     18  94% [L5F,T19R,K77T,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
..R..L.........D..G--.........RK.....R...N........      19      1      4     14      0      0      0      0      19     17  89% [T19R,P26L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..I.........I..D..G--.........RK.....R...N........      19     11      7      1      0      0      0      0      19     16  84% [T19I,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
F.R.........I..D..G--.........RK.....R...N...L....      19      0      0     15      4      0      0      0      19     13  68% [L5F,T19R,T95I,K97E,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] B.1.617.2=Delta
..R....S....I..D..G--.........RK.....R...N........      19      1      0      0     18      0      0      0      19     19 100% [T19R,T29S,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.......F.I.....G--.........RK.....R...N........      19      5     14      0      0      0      0      0      19     16  84% [T19R,V70F,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
..R...V...I....D..G--.........RK.....R...N........      19      0      0     19      0      0      0      0      19     17  89% [T19R,A27V,V70I,G142D,E156G,F157-,R158-,M177I,L452R,T478K,D614G,P681R,D950N] 
..R.........I..D..--..........RK.....R...N........      19      0     19      0      0      0      0      0      19     19 100% [T19R,T95I,G142D,S155R,E156-,F157-,L452R,T478K,D614G,P681R,D950N] 
..R.........I...SN.............K.........N........      19      0     19      0      0      0      0      0      19     19 100% [T19R,T95I,+143T,Y144S,Y145N,M153I,E154-,T478K,D614G,D950N] 
.................................Y...R............      19      0     19      0      0      0      0      0      19     19 100% [N501Y,D614G,P681R] 
............I.....................................      19      0     19      0      0      0      0      0      19     19 100% [T95I,D614G] 
FF..........I.............G.......................      18      0      0     18      0      0      0      0      18     15  83% [L5F,L18F,T95I,D253G,S477N,D614G,Q957R] B.1.526.2
..R............D..G--.........RKQ....R...N........      18      6      3      7      2      0      0      0      18     12  66% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--..........K.Y...R...N........      18      0     18      0      0      0      0      0      18     18 100% [T19R,E156G,F157-,R158-,T478K,N501Y,D614G,P681R,D950N] 
..R.......F.......G--.........RK.....R...N........      18      1      9      8      0      0      0      0      18     16  88% [T19R,V70F,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
F.R.........I.....G--.........RK.....R............      18      1      8      6      0      0      3      0      18     12  66% [L5F,T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
..R.....V.........G--.........RK.....R...N........      18      0      3     15      0      0      0      0      18     12  66% [T19R,A67V,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.....V...I..D..G--.........RK.....R.I.N........      18     18      0      0      0      0      0      0      18     17  94% [T19R,A67V,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T719I,D950N] B.1.617.2=Delta
.F.N.S........Y......VS......T..KY.Y.......I....F.      18      0      0     11      0      0      7      0      18     12  66% [L18F,T20N,P26S,D138Y,G181V,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
.F.......--.....-................YD..HI...A...H...      18      0      5     12      0      0      1      0      18     14  77% [L18F,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.........--.....-................Y....I...A.......      18      0     18      0      0      0      0      0      18     18 100% [H69-,V70-,Y144-,N501Y,D614G,T716I,S982A] 
.........--.....-................Y....I...........      18      0     18      0      0      0      0      0      18     18 100% [H69-,V70-,Y144-,N501Y,D614G,T716I] 
............I...........................L.........      18      0     18      0      0      0      0      0      18     18 100% [T95I,D614G,I850L] 
..R.........I.....................................      18      0     18      0      0      0      0      0      18     18 100% [T19R,T95I,D614G] 
.FR............D..G--..V......RK.....R...N........      17      0      5     12      0      0      0      0      17     13  76% [L18F,T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R......--.I..D..G--.........RK.....R...N........      17     14      3      0      0      0      0      0      17     11  64% [T19R,H69-,V70-,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
F.R...............G--..V...I..RK.....R...N........      17      0      0     17      0      0      0      0      17     17 100% [L5F,T19R,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I..D..G--V........RK.....R...N...L....      17      3      6      8      0      0      0      0      17     14  82% [T19R,T95I,G142D,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N,V1104L] B.1.617.2=Delta
F.R...S...........G--.........RK.....R...N........      17      0     17      0      0      0      0      0      17     11  64% [L5F,T19R,A27S,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R......--....D..G--.........RK.....R...N........      17      5      2      9      0      0      1      0      17     13  76% [T19R,H69-,V70-,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
..R...........................RKKY...R...N........      17      0     17      0      0      0      0      0      17     15  88% [T19R,L452R,T478K,E484K,N501Y,D614G,P681R,D950N] 
..R...........................RK.........N........      17      0     16      1      0      0      0      0      17     17 100% [T19R,L452R,T478K,D614G,D950N] 
.F.N.S........Y.......S.........KY.Y.......I....F.      17      0      4      8      0      0      5      0      17     10  58% [L18F,T20N,P26S,D138Y,R190S,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
..R...........YD..G--.........RK.....R...N........      16      2      5      9      0      0      0      0      16     15  93% [T19R,D138Y,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--........NRK.....R...N........      16      2      2     12      0      0      0      0      16     14  87% [T19R,G142D,E156G,F157-,R158-,K417N,L452R,T478K,D614G,P681R,D950N] 
..R.........I..D..G--.......I.RK.....R...N........      16      0      3     13      0      0      0      0      16     13  81% [T19R,T95I,G142D,E156G,F157-,R158-,R346I,L452R,T478K,D614G,P681R,D950N,K1073N] B.1.617.2=Delta
..R.........I.....G--................R...N........      16      0     13      3      0      0      0      0      16      9  56% [T19R,T95I,E156G,F157-,R158-,D614G,P681R,D950N] 
..R..S.........D..G--.........RK.....R...N........      16      4      7      5      0      0      0      0      16     14  87% [T19R,P26S,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--..V......RK.....R...N......F.      16      1     11      1      3      0      0      0      16     14  87% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1176F] Delta+A222V
..I............D..G--.........RK.....R...N........      16      6      7      3      0      0      0      0      16     12  75% [T19I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
..R........T...D..G--V........RK.....R...N........      16      0      0     16      0      0      0      0      16     14  87% [T19R,K77T,G142D,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--.........RK.....R.I.N........      16      0     14      1      1      0      0      0      16     15  93% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T719I,D950N] B.1.617.2=Delta
..R............D..G--................R...N........      16      0      3     13      0      0      0      0      16     13  81% [T19R,G142D,E156G,F157-,R158-,D614G,P681R,D950N] 
..R...............G--.........RKK....R...N........      16      0     11      5      0      0      0      0      16     15  93% [T19R,E156G,F157-,R158-,L452R,T478K,E484K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I....HG--..V......RK.....R...N........      16      6     10      0      0      0      0      0      16     15  93% [T19R,T95I,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R............D.......V......RK.....R...N........      16      0     10      0      6      0      0      0      16     12  75% [T19R,G142D,A222V,L452R,T478K,D614G,P681R,D950N] 
..I......--.....-................YD..HI...A...H...      16      0     11      3      2      0      0      0      16      9  56% [T19I,H69-,V70-,Y144-,K147E,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
F........--.....-................YD..HI...A...Y...      16      0      2     14      0      0      0      0      16     10  62% [L5F,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118Y] 
........S--.....-................YD..HI...A...H...      16      2      5      9      0      0      0      0      16      9  56% [A67S,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
..R.............................KY................      16      0     16      0      0      0      0      0      16     16 100% [T19R,E484K,N501Y,D614G] 
.............................N...Y................      15      0     15      0      0      0      0      0      15     14  93% [K417N,N501Y,D614G] 
...S....................---...Q...................      15      0      0     15      0      0      0      0      15     12  80% [T20S,G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,T859N] C.37=Lambda
..R............D..G--.........WK.....R...N........      15      1      6      8      0      0      0      0      15     15 100% [T19R,G142D,E156G,F157-,R158-,L452W,T478K,D614G,P681R,D950N] 
.FR...............G--.........RK.....R...N........      15      1      3      9      1      0      1      0      15     12  80% [L18F,T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R..L............G--.........RK.....R...N........      15      0      5      9      0      0      1      0      15     12  80% [T19R,P26L,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
F.R...............G--..V......RK.....R...N..S....L      15      0      0     15      0      0      0      0      15     14  93% [L5F,T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,N1074S,V1264L] Delta+A222V
F.R..........L.D..G--.........RK.....R...N........      15      0      0     15      0      0      0      0      15      9  60% [L5F,T19R,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.........I..D...--.........RK.....R...N........      15      0      2     13      0      0      0      0      15     14  93% [T19R,T95I,G142D,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
..R............................K.....R...N........      15      0     15      0      0      0      0      0      15     13  86% [T19R,T478K,D614G,P681R,D950N] 
.F.NIS........Y.......S......T..KY.Y.......I....F.      15      0      0     14      0      0      1      0      15     15 100% [L18F,T20N,R21I,P26S,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
.........--.....-....E...........YD..HI...A...H...      15      0     15      0      0      0      0      0      15     15 100% [H69-,V70-,Y144-,M153K,G181E,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,Q1201R] B.1.1.7=Alpha
..R.........I..D..G--R........RK.....R...N........      14     10      0      4      0      0      0      0      14      6  42% [T19R,T95I,G142D,E156G,F157-,R158-,G181R,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--.........RK.....R...N.....S..      14      0      3     11      0      0      0      0      14     12  85% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162S] B.1.617.2=Delta
..R............D..G--..V......RK....HR...N........      14      1      9      3      1      0      0      0      14     12  85% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,Q677H,P681R,D950N] Delta+A222V
..R.....V.........G--..V......RK.....R...N.......L      14      0      0     14      0      0      0      0      14     12  85% [T19R,A67V,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+A222V
..R...............G--..V......RK.....R...N.....S..      14      0      6      8      0      0      0      0      14     13  92% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,P1162S] Delta+A222V
............I.....G--.........RK.....R...N........      14      0     14      0      0      0      0      0      14      5  35% [T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
..RA..............G--..V...I..RK.....R...N........      14      0      0     14      0      0      0      0      14     13  92% [T19R,T20A,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R...............G--V........RK.....R............      14      0     12      1      0      0      1      0      14     13  92% [T19R,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R] 
..R...............G--.........RK.....R...N......F.      14      0     11      3      0      0      0      0      14      6  42% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,Q836E,D950N,V1176F] B.1.617.2=Delta
..R.........I.....G--.........RK.Y...R...N........      14      0     14      0      0      0      0      0      14      9  64% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681R,D950N] B.1.617.2=Delta
-.R............D..G--.........RK.....R...N........      14      0     12      2      0      0      0      0      14     10  71% [L5-,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R.......F.I..D..G--.........RK.....R..LN........      14      0     14      0      0      0      0      0      14     14 100% [T19R,V70F,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] 
..R....................V......RK.....R............      14      0      0      0     14      0      0      0      14      8  57% [T19R,A222V,L452R,T478K,D614G,P681R] 
........VS......................K.................      14      0     14      0      0      0      0      0      14     14 100% [A67V,H69S,E484K,D614G,F888L] 
.............................T..KY................      14      0     14      0      0      0      0      0      14     14 100% [K417T,E484K,N501Y,D614G] 
.........--......................YD..HI...A...H...      14      0     10      1      3      0      0      0      14      7  50% [H69-,V70-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
................................KY.......N........      14      0     14      0      0      0      0      0      14      9  64% [E484K,N501Y,D614G,D950N] 
.R..........I.......S...........Q....H.....I......      13      0      2     11      0      0      0      0      13      5  38% [L18R,T95I,R158S,N440K,E484Q,D614G,P681H,A688V,S735A,T1027I] 
..R...S.....I.....G--.........RK.....R............      13      0      1     12      0      0      0      0      13     10  76% [T19R,A27S,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
F.R...............G--..V......RK.....R...N.......L      13      0      0     12      1      0      0      0      13     10  76% [L5F,T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+A222V
..R.........I.....G--.........RK.....R..L.........      13      0      9      1      3      0      0      0      13      5  38% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L] 
..R.........I..D-DG--.........RK.....R...N........      13     12      1      0      0      0      0      0      13      8  61% [T19R,T95I,A123T,G142D,V143-,Y144-,Y145D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--....................N........      13      0     13      0      0      0      0      0      13     12  92% [T19R,G142D,E156G,F157-,R158-,D614G,D950N] 
F.R........T......G--.........RKQ....R...N........      13      0      0     13      0      0      0      0      13     12  92% [L5F,T19R,K77T,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
..R........T...D..G--.........RK.....R...N.....S..      13      0      0     13      0      0      0      0      13     13 100% [T19R,K77T,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,P1162S] B.1.617.2=Delta
F.R.........I.....G--.........RK.....R..LN........      13      0     13      0      0      0      0      0      13     11  84% [L5F,T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] B.1.617.2=Delta
...................S..........R......R............      13      0     13      0      0      0      0      0      13     13 100% [F157S,L452R,D614G,P681R] 
................-......V......RRQ..Y.....N........      13      0      1     12      0      0      0      0      13      9  69% [P9L,C136F,Y144-,A222V,A243-,L244-,L452R,T478R,E484Q,D614G,H655Y,D950N] 
.F.N.S........Y..............T..KY.Y.......I....F.      13      0      1      2      0      0     10      0      13      8  61% [L18F,T20N,P26S,D138Y,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] 
.F.N.S........---.....S......T..KY.Y.......I....F.      13      0      0      1      0      0     12      0      13      9  69% [L18F,T20N,P26S,D138-,P139Y,F140-,L141-,G142-,V143-,Y144-,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
...I............................K..........I......      13      0      0      0     13      0      0      0      13     12  92% [T20I,I210T,N440K,E484K,D614G,D936N,S939F,T1027I] B.1.619
................................................F.      13      0     13      0      0      0      0      0      13     13 100% [D614G,V1176F] 
................................K........N........      12      0     12      0      0      0      0      0      12      8  66% [N440K,E484K,D614G,D936N,S939F,D950N] 
..............................RK.Y................      12      0     12      0      0      0      0      0      12     12 100% [L452R,T478K,N501Y,D614G] 
.RI.........I.......S................H.....I......      12      0      2     10      0      0      0      0      12      8  66% [L18R,T19I,T95I,R158S,N440K,D614G,P681H,A688V,S735A,S939F,T1027I] 
..............H.........---...Q...................      12      0      0     12      0      0      0      0      12      6  50% [G75V,T76I,D138H,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,T859N,A1020S] C.37=Lambda
F.......................---...Q...................      12      0      0      1      0      0     11      0      12      9  75% [L5F,G75V,T76I,R246N,S247-,Y248-,L249-,T250-,P251-,G252-,D253-,L452Q,F490S,D614G,T859N] C.37=Lambda
............I...SN..........KN..KY...H............      12      0      0     12      0      0      0      0      12      5  41% [T95I,+143T,Y144S,Y145N,R346K,K417N,E484K,N501Y,D614G,P681H] 
..............................RKKY...R............      12      0     12      0      0      0      0      0      12     10  83% [L452R,T478K,E484K,N501Y,D614G,P681R] 
..R............D..G--.........R......R...N........      12      0     10      2      0      0      0      0      12     10  83% [T19R,G142D,E156G,F157-,R158-,L452R,D614G,P681R,D950N] 
..R............D..G--......I..RK.....R...N........      12      1      1     10      0      0      0      0      12     11  91% [T19R,G142D,E156G,F157-,R158-,V289I,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--....L....RK.....R............      12      0     12      0      0      0      0      0      12     11  91% [T19R,G142D,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R] 
..R...............G--.........RKQ....R...N........      12      0      4      5      3      0      0      0      12      8  66% [T19R,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--.........RK.....R...N.......F      12      0      0      1     11      0      0      0      12     10  83% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264F] B.1.617.2=Delta
.F.N.S...--...Y.......S......T..KY.Y.......I....F.      12      0      0      0      0      0     12      0      12      8  66% [L18F,T20N,P26S,H69-,V70-,D138Y,R190S,K417T,E484K,N501Y,D614G,H655Y,Q675H,T1027I,V1176F] P.1=Gamma
.........--.....-................Y...HI...A...H...      12      0      8      3      1      0      0      0      12      8  66% [H69-,V70-,Y144-,N501Y,D614G,P681H,T716I,S982A,D1118H] 
..R...........................RK..................      12      0     11      1      0      0      0      0      12     12 100% [T19R,L452R,T478K,D614G] 
..R.........I.................RK..................      12      0     12      0      0      0      0      0      12     12 100% [T19R,T95I,L452R,T478K,D614G] 
..R.............................K....R...N........      12      0     12      0      0      0      0      0      12     12 100% [T19R,E484K,D614G,P681R,D950N] 
..................G--..........K.....R...N........      11      0      9      2      0      0      0      0      11     11 100% [E156G,F157-,R158-,T478K,D614G,P681R,D950N] 
..R...............G--.........RK.........N........      11      0     10      1      0      0      0      0      11      6  54% [T19R,E156G,F157-,R158-,N440K,L452R,T478K,D614G,D950N] 
..R...............G--..........K.....R..LN........      11      0     11      0      0      0      0      0      11     10  90% [T19R,E156G,F157-,R158-,T478K,D614G,P681R,I850L,D950N] 
..R........TI..D..G--.........RK.....R...N........      11      0      0     11      0      0      0      0      11     10  90% [T19R,K77T,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--.........RK.....L...N........      11      5      3      3      0      0      0      0      11      6  54% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681L,D950N] 
..R............D..G--..V......RKQ....R...N........      11      0     11      0      0      0      0      0      11     11 100% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,E484Q,D614G,P681R,D950N] Delta+A222V
..R......Y.....D..G--..V......RK.....R...N........      11      2      9      0      0      0      0      0      11     10  90% [T19R,H69Y,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
F.R...............G--..V......RK.....R............      11      0      0      2      9      0      0      0      11      6  54% [L5F,T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R] 
..R.........I.....G--..S......RK.....R...N........      11      1      9      1      0      0      0      0      11     10  90% [T19R,T95I,E156G,F157-,R158-,A222S,L452R,T478K,D614G,P681R,D950N] 
..R...............G--..V...L..RK.....R...N........      11      0      5      0      6      0      0      0      11      5  45% [T19R,E156G,F157-,R158-,A222V,V289L,L452R,T478K,D614G,P681R,D950N] Delta+A222V
F.R............D..G--.........RK.....R...N.......L      11      0      0      2      9      0      0      0      11     11 100% [L5F,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
.F......V--.....................KT................      11      0      3      8      0      0      0      0      11      9  81% [L18F,A67V,I68-,H69-,V70-,G257S,E484K,F490S,N501T,D614G,T859N] 
.........--.....-................YDY.HI...A...H...      11      0      5      5      1      0      0      0      11      5  45% [H69-,V70-,Y144-,N501Y,A570D,D614G,H655Y,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.................................Y.Y..............      11      0     11      0      0      0      0      0      11     11 100% [Y449H,N501Y,F565L,H655Y] 
..............Y...................................      10      0      9      1      0      0      0      0      10      9  90% [D138Y,S477N,A522S,D614G,Q675R,A845S] 
..R............D..G--.........RK.....R...N....Y...      10      1      2      5      2      0      0      0      10      8  80% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,D1118Y] B.1.617.2=Delta
..R............D..G--...I.....RK.....R...N........      10      1      6      1      0      2      0      0      10      4  40% [T19R,G142D,E156G,F157-,R158-,T250I,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...............G--.........RK.....R...N....Y...      10      0      6      1      3      0      0      0      10      7  70% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,D1118Y] B.1.617.2=Delta
..R......Y........G--.........RK.....R...N........      10      0      7      2      0      0      1      0      10      6  60% [T19R,H69Y,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...........YD..G--..V......RK.....R...N........      10      8      2      0      0      0      0      0      10      9  90% [T19R,D138Y,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+A222V
..R.........I..D..G--.........RK..S..R...N........      10      5      3      2      0      0      0      0      10      3  30% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,A570S,D614G,P681R,D950N] B.1.617.2=Delta
F.R.........I.....G--.........RK.....R...N...L....      10      0      1      9      0      0      0      0      10      7  70% [L5F,T19R,T95I,K97E,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1104L] B.1.617.2=Delta
..R.........I..D..G--..V......RK.....R...N...L....      10      1      1      8      0      0      0      0      10      9  90% [T19R,T95I,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1104L] Delta+A222V
..R.........I..D..G--.........RK.....R...N....Y...      10      4      1      4      1      0      0      0      10      8  80% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,D1118Y] B.1.617.2=Delta
..R........T......G--V........RK.....R...N........      10      0      0     10      0      0      0      0      10      5  50% [T19R,K77T,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R........R...D..G--.........RK.....R...N.......L      10      0      0      0     10      0      0      0      10     10 100% [T19R,K77R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] B.1.617.2=Delta
..R.I..........D..G--....L....RK.....R...N........      10      2      8      0      0      0      0      0      10     10 100% [T19R,R21I,G142D,E156G,F157-,R158-,P251L,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R............D..G--.........RK.....R...N.I......      10      0      1      9      0      0      0      0      10      7  70% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,T1027I] B.1.617.2=Delta
..R.........I.....G--.........RK.....RI..N........      10      1      9      0      0      0      0      0      10     10 100% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T716I,D950N] B.1.617.2=Delta
..R.........I..D..G--.........RK.....L...N........      10      4      5      0      1      0      0      0      10      9  90% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681L,D950N] 
..R............D..G--.....A...RK.....R...N........      10      0      8      2      0      0      0      0      10     10 100% [T19R,G142D,E156G,F157-,R158-,D253A,L452R,T478K,D614G,P681R,D950N] B.1.617.2=Delta
..R...........................RK..S..R...N........      10      0     10      0      0      0      0      0      10     10 100% [T19R,L452R,T478K,A570S,D614G,P681R,D950N] 
..R...........................RK.Y.......N........      10      0     10      0      0      0      0      0      10     10 100% [T19R,L452R,T478K,N501Y,D614G,D950N] 
....................................H.............      10      0      9      1      0      0      0      0      10      7  70% [D614G,Q677H] Near-Furin
.F.N.S........Y.-.....S......T..KY.Y.......I....F.      10      0      0      2      0      0      8      0      10      5  50% [L18F,T20N,P26S,D138Y,Y144-,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
.F.N.S........Y--.....S......T..KY.Y.......I....F.      10      0      0      5      0      0      5      0      10      7  70% [L18F,T20N,P26S,D138Y,L141-,G142-,V143-,Y144-,R190S,K417T,E484K,N501Y,D614G,H655Y,T1027I,V1176F] P.1=Gamma
.............................T..KY.........I......      10      0     10      0      0      0      0      0      10     10 100% [K417T,E484K,N501Y,D614G,T1027I] 
.........--.....-................YD..HI...A...H..L      10      0      4      2      4      0      0      0      10      5  50% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H,V1264L] B.1.1.7=Alpha
.........--.....-.........G......YD..HI...A...H...      10      0      5      3      2      0      0      0      10      7  70% [H69-,V70-,Y144-,D253G,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] B.1.1.7=Alpha
.....H...--.....-................YD..HI...A...H...      10      0      0     10      0      0      0      0      10      7  70% [P26H,H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,A684V,T716I,L938F,S982A,D1118H] B.1.1.7=Alpha
..................V--...........K..........I......      10      0     10      0      0      0      0      0      10      7  70% [E156V,F157-,R158-,V159-,F306L,E484K,S494P,D614G,E780A,D839V,T1027I] 
......S......................N..KY................      10      2      0      4      4      0      0      0      10      4  40% [A27S,D80A,D215G,L242-,A243-,L244-,K417N,E484K,N501Y,D614G,A701V] B.1.351=Beta
..R.........I..................K.....R...N........      10      0     10      0      0      0      0      0      10      8  80% [T19R,T95I,T478K,D614G,P681R,D950N] 
.F.N.S.......................T..KY..............F.      10      0     10      0      0      0      0      0      10     10 100% [L18F,T20N,P26S,K417T,E484K,N501Y,D614G,V1176F] 
.........--.....-.............RK..D..HI...A...H...      10      0     10      0      0      0      0      0      10      4  40% [H69-,V70-,Y144-,L452R,T478K,A570D,D614G,P681H,T716I,S982A,D1118H] 
..............................RK.Y...R...N........      10      0     10      0      0      0      0      0      10     10 100% [L452R,T478K,N501Y,D614G,P681R,D950N] 

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last modified: Fri Sep 10 02:06 2021



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