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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: Jan 20, 2022
 

Delta and Omicron, Jan 2022 Variants
Global
Early 2021 Variants color key
Delta Variants color key

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Evaluating 593155 sequences of length 2749
Sampled from 2021-11-21 to 2022-01-14.
Specified Date Range: (datetime.date(2021, 11, 21), datetime.date(2022, 1, 20))
Highest entropy sites for: Global
  Site Entropy
    95  0.6874
   145  0.6316
   222  0.3771
    19  0.3749
    70  0.3684
   484  0.3670
   156  0.3546
   371  0.3535
   158  0.3532
   950  0.3531
   157  0.3530
   477  0.3459
   679  0.3454
   681  0.3449
   211  0.3432
   796  0.3429
   655  0.3421
   212  0.3420
    67  0.3407
   452  0.3403
    69  0.3393
   954  0.3387
   969  0.3383
   764  0.3368
   501  0.3355
   339  0.3350
   547  0.3348
   446  0.3347
   373  0.3324
   143  0.3319
   144  0.3316
   375  0.3311
   493  0.3304
   505  0.3292
   498  0.3290
   440  0.3264
   856  0.3259
   981  0.3248
   417  0.3201
   496  0.3160
   214  0.0157
   142  0.2670
   346  0.1567
  1264  0.1471
     5  0.0838
    36  0.0818
   112  0.0741
   850  0.0683


Most highly correlated site-pairs for: Global
               cramerV  mutInfo
   156    158   0.7099   0.3521
   156    157   0.5772   0.3517
   158    157   0.7072   0.3509
   211    212   0.7715   0.3399
   954    969   0.9993   0.3371
   679    954   0.5761   0.3350
   679    969   0.9978   0.3349
   679    681   0.4934   0.3328
   681    954   0.5739   0.3314
   681    969   0.9940   0.3313
   954    764   0.9949   0.3308
   796    954   0.5742   0.3307
   796    969   0.9946   0.3307
   969    764   0.9949   0.3306
   679    764   0.9947   0.3304


   493    498   0.9978   0.3258
   505    498   0.9972   0.3248
   501    498   0.9941   0.3222
   796    764   0.9932   0.3285
   681    764   0.9909   0.3274
   655    969   0.9897   0.3272
   655    764   0.9862   0.3231
   484    498   0.9855   0.3140
   477    498   0.9854   0.3136
   969    339   0.9844   0.3181
   764    339   0.9822   0.3147
   452    969   0.9819   0.3170
   452    764   0.9813   0.3158
   339    498   0.9794   0.3085
   371    498   0.9793   0.3067


Most common patterns for local area, where Local = Global
                                               1
       11111111222233333444444444555666778899992
 13667914444555111234777144578999004578695555686
596790522345678124296135706274368157591460604914
LTVAHVTSGVYYEFRNLRAGRSSSKNGLSEQGQNYTHNPNDINDQNLV  Global     UK  Eu-UK  NAmer   Asia Africa  SAmer  Ocean   Local  Exact  Pct [Context]
                                                  593155 192375 164111 206074  14956   1546   5903   8190  593155 <----------- Totals
.R......D...G--............R..........R....N....  190039  31233  54427 101028   2180    153    938     80  190039 113614  59% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--............R..........R....N....  185000  99321  42956  34456   2303     83    544   5337  185000  96360  52% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D..HG--...V........R..........R....N....   31124  27681   3320     85     31      2      1      4   31124  21809  70% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
...V--I.D---...-I..D.LPFNKS.NARSRYHKYKHKY.K.HKF.   28359    556   6889  16222   1251    871    519   2051   28359  24255  85% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
.R..........G--............R..........R....N....   17718     42  10849   3687   1507      0   1628      5   17718  10599  59% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---...-I..DKLPFNKS.NARSRYHKYKHKY.K.HKF.   16853     81   1753  13425   1112     66    174    242   16853  16142  95% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
.R....I.D..HG--...V........R..........R....N...L   13169  12897    221     29     17      4      0      1   13169   7613  57% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+Y145H,A222V
.R....I.....G--............R..........R....N....   11618    120   8026   1741    751      5    865    110   11618   5695  49% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.RF...I.D..HG--...V........R..........R....N....    8874   8555    221     91      6      0      0      1    8874   7118  80% [T19R,V36F,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
.R......D...G--...V........R..........R....N....    8862   1001   2500   4007   1303      1     43      7    8862   4026  45% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
.R.....LD...G--............R..........R....N....    7344     65    106   7168      2      0      3      0    7344   5278  71% [T19R,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta+S112L
.R....I.D...G--............R..........R..L.N....    5239    425   4573    187     37      1     12      4    5239   3004  57% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] Delta
FR....I.D...G--............R..........R....N....    3877   1760   1435    619     17      0      6     40    3877   2206  56% [L5F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.I......D..........D.FPFNK..NAR.RYH.YKHKY...HK..    3495     19   3292      3    134     40      1      6    3495   2832  81% [T19I,L24S,P25-,P26-,A27-,G142D,V213G,G339D,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,S477N,T478K,E484A,Q493R,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] Omicron_BA.2
...V--I.D---...I-..D.LPFNKS.NARSRYHKYKHKY.K.HKF.    3148     14   1346   1447      7    172    152     10    3148   2525  80% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
FR......D...G--............R..........R....N....    2907    464   1126   1277     17      4     19      0    2907   1630  56% [L5F,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R...I..D...G--............R..........R....N....    1968     10      6   1950      1      0      1      0    1968    850  43% [T19R,V70I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
.R......D...G--............R..........R....N...L    1922    297    278    398    933      1      7      8    1922   1059  55% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+V1264L
.R..........G--...V........R..........R....N....    1868      1    495     59   1276      0     37      0    1868   1338  71% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
.R......D...G--...V........R..........R....N...L    1826     22    189   1575     36      2      1      1    1826    738  40% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+V1264L
...........................R..........R....N....    1381      0    183   1198      0      0      0      0    1381    894  64% [L452R,T478K,D614G,P681R,D950N] 
...V--I.D---.......D.LPFNKS.NARSRYHKYKHKY.K.HKF.    1352      0   1343      8      0      0      0      1    1352    911  67% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
.R..........G--............R..........R.........    1326      0    984     81     80      1    180      0    1326    722  54% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
.R....I.....G--............R..........R..L.N....    1218      0   1191      5     21      0      0      1    1218    630  51% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] Delta
.R....I.D...G--............R.Q........R....N....    1086    320    607     99     56      1      1      2    1086    358  32% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] 
.R.........................R..........R....N....     900      0    151    734      9      0      6      0     900    533  59% [T19R,L452R,T478K,D614G,P681R,D950N] 
.R....I.D...G--............R..........R....N...L     843    346    178    289     27      0      1      2     843    395  46% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+V1264L
.R....I.....G--............R..........R.........     784      1    664     62     13      0     44      0     784    369  47% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
...V--I.D---...-I..D.LPF.KS.NARSRYHKYKHKY.K.HKF.     758      0    434    297      7      6     14      0     758    649  85% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
...V--I.D---.......................KYKHKY.K.HKF.     742      0      0    742      0      0      0      0     742    718  96% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
FR....I.D..HG--...V........R..........R....N....     707    457    249      1      0      0      0      0     707    334  47% [L5F,T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
...V--I.D---...I-..DKLPFNKS.NARSRYHKYKHKY.K.HKF.     620      0    196    377      4      5     34      4     620    593  95% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
.R....I.D...G--...........VR..........R....N....     595    192    103    143     44      0      4    109     595    412  69% [T19R,T95I,G142D,E156G,F157-,R158-,G446V,L452R,T478K,D614G,P681R,D950N] Delta
.R.V....D...G--............R..........R....N....     562    286     94    177      3      0      2      0     562    268  47% [T19R,A67V,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---...-I..DKLPF.KS.NARSRYHKYKHKY.K.HKF.     503      0    227    241     10     17      8      0     503    481  95% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
.R......D...G--............R.Q........R....N....     503     52    187    247     12      0      5      0     503    201  39% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] 
.R......D...G--............R.A........R....N....     475     15    426     25      8      0      0      1     475    256  53% [T19R,G142D,E156G,F157-,R158-,G181V,L452R,T478K,E484A,D614G,P681R,D950N] 
.R....I.D...G--...S........R..........R....N....     475    100    297     47      9      0      1     21     475    306  64% [T19R,T95I,G142D,E156G,F157-,R158-,A222S,L452R,T478K,D614G,P681R,D950N] 
.R....I.D...G--...V........R..........R....N....     436    111    159    108     15      0     42      1     436    112  25% [T19R,T95I,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] 
.R..Y.I.D...G--............R..........R....N....     436     62    357     11      4      1      0      1     436    248  56% [T19R,H69Y,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I....HG--...V........R..........R....N....     432     35    393      1      2      0      1      0     432    276  63% [T19R,T95I,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
.R......D...G--............RI.........R....N....     427    125    229     71      1      0      1      0     427    158  37% [T19R,G142D,E156G,F157-,R158-,L452R,S477I,T478K,D614G,P681R,D950N] Delta
.R......D...G--...........VR..........R....N....     424     57    153    209      3      0      2      0     424    269  63% [T19R,G142D,E156G,F157-,R158-,G446V,L452R,T478K,D614G,P681R,D950N] Delta
.R.S....D...G--............R..........R....N....     419    179    181     56      2      0      0      1     419    324  77% [T19R,A67S,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---...-I..D.LPF...RNARSRYHKYKHKY.K.HKF.     408     20     30    357      1      0      0      0     408    369  90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,L452R,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+417_,440_,446_,L452R
.R....I.D...G--............R........Y.R....N....     404    330     43     29      1      0      0      1     404    232  57% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,H655Y,P681R,D950N] Delta+FurinRelated
FR..........G--............R..........R....N....     394      1    292     47     11      0     43      0     394    229  58% [L5F,T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R......D.-.G--............R..........R....N....     391    128     69    186      3      0      5      0     391    234  59% [T19R,G142D,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--............R..........R.........     375      6    159    185      7      0     18      0     375    211  56% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
.R...FI.D...G--............R..........R....N....     372    298     56      8      3      0      1      6     372    263  70% [T19R,V70F,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
.R...II.D..HG--...V........R..........R....N....     359      8    351      0      0      0      0      0     359    321  89% [T19R,V70I,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] 
.R....I.D.-.G--............R..........R....N....     348    147    156     42      3      0      0      0     348    193  55% [T19R,T95I,G142D,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---...I-..D.LPF.KS.NARSRYHKYKHKY.K.HKF.     344      0     99    245      0      0      0      0     344    297  86% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,S371L,S373P,S375F,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
.R...F..D...G--............R..........R....N....     339      6     31    302      0      0      0      0     339    306  90% [T19R,V70F,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
...V..I.D---.......D.LPFNKS.NARSRYHKYKHKY.K.HKF.     304      0    304      0      0      0      0      0     304    239  78% [A67V,T95I,G142D,V143-,Y144-,Y145-,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R....I.D...G--..L.........R..........R....N....     300    220     26     49      4      0      0      1     300    200  66% [T19R,T95I,G142D,E156G,F157-,R158-,R214L,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--..L.........R..........R....N....     297     25    139    124      9      0      0      0     297    224  75% [T19R,G142D,E156G,F157-,R158-,R214L,L452R,T478K,D614G,P681R,D950N] Delta
FR....I.....G--............R..........R....N....     297      1    234     35     17      0     10      0     297    142  47% [L5F,T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--............R........Y.R....N....     286     27     58    194      5      0      2      0     286    204  71% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,H655Y,P681R,D950N] Delta+FurinRelated
.R....I.D...G--............R.Q........R..L.N....     285      1    283      1      0      0      0      0     285    221  77% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,I850L,D950N] 
.R..Y...D...G--............R..........R....N....     279     30    116    131      1      0      1      0     279    226  81% [T19R,H69Y,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--............RI.........R....N....     270    122     37     85     25      0      0      1     270    147  54% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,S477I,T478K,D614G,P681R,D950N] Delta
.R......D...G--............R.......I..R....N....     258     64     52    140      0      0      2      0     258    140  54% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,T547I,D614G,P681R,D950N] Delta
.R....I.D...G--............RN.........R....N....     247    102    123     22      0      0      0      0     247    195  78% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,S477N,T478K,D614G,P681R,D950N] Delta
...V--I.D---...-I..D.LPF....NARSRYHKYKHKY.K.HKF.     245      2     60    183      0      0      0      0     245    221  90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
.R......D...G--.....K......R..........R....N....     244     16    182     24     22      0      0      0     244     76  31% [T19R,T29A,G142D,E156G,F157-,R158-,T250I,R346K,L452R,T478K,D614G,P681R,P812L,D950N] 
.R.V..I.D...G--............R..........R....N....     243    124     86     33      0      0      0      0     243    136  55% [T19R,A67V,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---...-I..D.LPFN.S.NARSRYHKYKHKY.K.HKF.     242      0    161     42     20      0     19      0     242    191  78% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
.R..........G--...V........R..........R.........     235      0     60      4    171      0      0      0     235    175  74% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R] 
.R....I.D...G--.........N..R..........R....N....     216     81     11    122      2      0      0      0     216     85  39% [T19R,T95I,G142D,E156G,F157-,R158-,W258L,K417N,L452R,T478K,D614G,P681R,D950N] 
.R.....L....G--............R..........R....N....     208      0      6    200      1      0      1      0     208    137  65% [T19R,S112L,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta+S112L
.R..........G--...V........R..........R....N...L     200      0     42    149      2      1      5      1     200     95  47% [T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+V1264L
.R...FI.D..HG--...V........R..........R....N....     197    197      0      0      0      0      0      0     197    173  87% [T19R,V70F,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] 
...V--I.D---...-I..DKLPF....NARSRYHKYKHKY.K.HKF.     194      0     22    172      0      0      0      0     194    188  96% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
.R....I.D...G--............R.K........R....N....     190     47    120     11     12      0      0      0     190     86  45% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484K,D614G,S673T,P681R,D950N] 
.R....I.D..................R..........R....N....     185      0    119     42     24      0      0      0     185     95  51% [T19R,T95I,G142D,L452R,T478K,D614G,P681R,D950N] 
.R..--I.D...G--............R..........R....N....     185     52    111      8      0      0      0     14     185    132  71% [T19R,H69-,V70-,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
.R....I.....G--............R.Q........R....N....     174      2    138      9     20      3      2      0     174    106  60% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] 
.R.S..I.D...G--............R..........R....N....     168    121     13     27      7      0      0      0     168    108  64% [T19R,A67S,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
FR....I.D..HG--...V........R..........R....N...L     166    162      4      0      0      0      0      0     166     97  58% [L5F,T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+Y145H,A222V
.R......D...G--............R..........H....N....     165      1      9    155      0      0      0      0     165    147  89% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681H,D950N] Delta+FurinRelated
.R......D...G--..H.........R..........R....N....     164      0      4    160      0      0      0      0     164    126  76% [T19R,G142D,E156G,F157-,R158-,R214H,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---...............RNARSRYHKYKHKY.K.HKF.     163      0    163      0      0      0      0      0     163    153  93% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,L452R,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
............G--............R..........R....N....     163      0      9    153      0      0      1      0     163    105  64% [E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
.R.V....D...G--...V........R..........R....N....     162     65     60      2      7      0     28      0     162    111  68% [T19R,A67V,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
...V--I.D---...-I..D.LPF.KS........KYKHKY.K.HKF.     157      0      0    157      0      0      0      0     157    149  94% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,N440K,G446S,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R......D...G--............R.....Y....R....N....     157      0     24     21    112      0      0      0     157    104  66% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681R,D950N] Delta
.R..--..D...G--............R..........R....N....     156     10     16    105     24      0      1      0     156     69  44% [T19R,H69-,V70-,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
.R......D...G--............RN.........R....N....     152      1     80     70      1      0      0      0     152    138  90% [T19R,G142D,E156G,F157-,R158-,L452R,S477N,T478K,D614G,P681R,D950N] Delta
.R..........G--............R..........R....N...L     152      0     97      5      8      0     38      4     152     89  58% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+V1264L
.R....I.D..HG--...V........R.........IR....N...L     152    152      0      0      0      0      0      0     152     94  61% [S13T,T19R,T95I,S98F,G142D,Y145H,E156G,F157-,R158-,A222V,T323I,L452R,T478K,D614G,N679I,P681R,D950N,V1264L] Delta+FurinRelated
.R......D..................R..........R....N....     139      0     60     71      8      0      0      0     139     77  55% [T19R,G142D,L452R,T478K,D614G,P681R,D950N] 
.R....I.....G--...V........R..........R....N....     138      0     54      4     11      0     69      0     138     46  33% [T19R,T95I,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,I834T,D950N] 
.R....I.D...G--............R.A........R....N....     137      3     40     90      3      1      0      0     137     67  48% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484A,D614G,P681R,D950N] 
......................................R....N....     136      0    123     13      0      0      0      0     136     87  63% [T478K,D614G,P681R,D950N] 
.R..........G--............R.Q........R....N....     136      0    119      7      0      0     10      0     136     97  71% [T19R,E156G,F157-,R158-,L452R,T478K,E484Q,Q613H,D614G,P681R,D950N] 
.RF...I.D...G--............R..........R....N....     133     79     12     40      1      0      0      1     133     77  57% [T19R,V36F,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---...-I..D.LPFNKS.NA.....KYKHKY.K.HKF.     129      1      3    125      0      0      0      0     129    116  89% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R......D...G--...V........R.......I..R....N....     118      1      2    100     14      0      1      0     118     66  55% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,T547I,D614G,P681R,D950N] Delta+T95_,A222V
...V--I.D---...-I..D.LPFNKS........KYKHKY.K.HKF.     115      0      1    113      1      0      0      0     115    104  90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..DKLPFNKS.NA.....KYKHKY.K.HKF.     114      0      1    113      0      0      0      0     114    109  95% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R....I.D...G--............R..........R.........     112      2     62     42      1      0      5      0     112     43  38% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
FR.....LD...G--............R..........R....N....     111      0      1    108      0      0      2      0     111     95  85% [L5F,T19R,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta+S112L
.R......D..HG--............R..........R....N....     107      5     34     68      0      0      0      0     107     37  34% [T19R,G142D,Y145H,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.DF..G--............R..........R....N....     107     63     26     15      3      0      0      0     107     51  47% [T19R,L54F,T95I,G142D,V143F,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--............R..........R.Y..N....     107     78     13     16      0      0      0      0     107     56  52% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D796Y,D950N] Delta
.R......D...G--...S........R..........R....N....     106     41     17     48      0      0      0      0     106     47  44% [T19R,G142D,E156G,F157-,R158-,A222S,L452R,T478K,D614G,P681R,D950N] 
.R......D...G--............R.........TR....N....     104      2      5     96      0      0      1      0     104     69  66% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,N679T,S680-,P681R,D950N,T1117I] Delta+FurinRelated
...V--I.D---...-I..DKLPF.KS........KYKHKY.K.HKF.     102      0      0    101      1      0      0      0     102     97  95% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,N440K,G446S,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---.......D...............KYKHKY.K.HKF.     101      0      1    100      0      0      0      0     101     91  90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,G339D,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...I-..DKLPF.KS.NARSRYHKYKHKY.K.HKF.     101      0     54     46      0      0      1      0     101     87  86% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,R346K,S371L,S373P,S375F,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
........D...G--............R..........R....N....     100      1     23     64     10      2      0      0     100     48  48% [G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
FR......D...G--...V........R..........R....N....      97      8     40     40      9      0      0      0      97     30  30% [L5F,T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
......I.D...G--............R..........R....N....      95      6     27     22     35      0      0      5      95     52  54% [T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
........---.........S............Y....H.........      94      7     82      4      0      1      0      0      94     78  82% [P9L,E96Q,C136-,N137-,D138-,P139-,F140-,L141-,G142-,V143-,Y144-,R190S,I210T,R346S,N394S,Y449N,F490R,N501Y,D614G,P681H,T859N,D936H] B.1.640.1
.R....I.D...G--I-..........R..........R....N....      91     86      2      3      0      0      0      0      91     22  24% [T19R,T95I,G142D,E156G,F157-,R158-,N211I,L212-,L452R,T478K,D614G,P681R,D950N,V1094I] Delta
F..V--I.D---...-I..D.LPFNKS.NARSRYHKYKHKY.K.HKF.      90      0     25     50      6      3      4      2      90     80  88% [L5F,A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
.R....I.D...G--.....I......R..........R....N....      90      4      4     79      0      0      0      3      90     64  71% [T19R,T95I,G142D,E156G,F157-,R158-,R346I,L452R,T478K,D614G,P681R,D950N,K1073N] Delta
.R....................................R....N....      89      0     65     24      0      0      0      0      89     49  55% [T19R,T478K,D614G,P681R,D950N] 
...V--I.D---...-I..DKLPFN.S.NARSRYHKYKHKY.K.HKF.      89      0     48     27     11      0      3      0      89     83  93% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
FR....I.D...G--............R..........R..L.N....      89      5     81      1      2      0      0      0      89     54  60% [L5F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] Delta
...V--I.D---...-I..DKLPFNKS........KYKHKY.K.HKF.      86      0      0     86      0      0      0      0      86     80  93% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R......D...G--.......................R....N....      86      0     27     54      5      0      0      0      86     30  34% [T19R,G142D,E156G,F157-,R158-,T478K,D614G,P681R,D950N] 
...V--I.D---...-I..D.LPF...RNARSRYHKYKH.Y.K.HKF.      85     43     17     24      0      1      0      0      85     72  84% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,L452R,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,D796Y,N856K,Q954H,N969K,L981F] 
.R....I.D...G--............R..........R.G..N....      84      0     80      4      0      0      0      0      84     69  82% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D796G,D950N,D1259Y] Delta
.R......D...G--............R.....S....R....N....      84      0     80      3      1      0      0      0      84     77  91% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,N501S,D614G,P681R,D950N] Delta
...V--I.D---...-I.......NKS.NARSRYHKYKHKY.K.HKF.      83      0      0     83      0      0      0      0      83     74  89% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R...I......G--............R..........R....N....      83      0      0     80      2      0      1      0      83     29  34% [T19R,V70I,E156G,F157-,R158-,Q414R,L452R,T478K,D614G,P681R,D950N] 
.R....I.D--DG--............R..........R....N....      81     77      1      2      1      0      0      0      81     67  82% [T19R,T95I,G142D,V143-,Y144-,Y145D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R..........G--............RI.........R....N....      80      0     70      1      0      0      9      0      80     38  47% [T19R,E156G,F157-,R158-,A262S,L452R,S477I,T478K,D614G,P681R,D950N,G1167V] Delta
.R....I.D...G--............R.......I..R....N....      80     37     14     28      1      0      0      0      80     32  40% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,T547I,D614G,P681R,D950N] Delta
.R....I.D...G--............R..........R.H..N....      80     12     59      6      2      0      0      1      80     39  48% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D796H,D950N,D1259Y] Delta
.R....I.....G--............R..........R..L......      80      0     80      0      0      0      0      0      80     50  62% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L] 
.R....I.D...G--..H.........R..........R....N....      79     37      5     37      0      0      0      0      79     64  81% [T19R,T95I,G142D,E156G,F157-,R158-,R214H,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---.......DKLPFNKS.NARSRYHKYKHKY.K.HKF.      78      0     77      1      0      0      0      0      78     65  83% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
.R....I.....G--............R..........R....N...L      78      0     56      9     10      0      3      0      78     35  44% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+V1264L
.R......D...G--............R..........R....N...M      78      6     36     35      0      0      1      0      78     61  78% [T19R,G142D,E156G,F157-,R158-,W258L,L452R,T478K,D614G,P681R,D950N,V1264M] 
...V--I.D---...-I..D.LPFNKS.NARSRYHKYKH.Y.K.HKF.      77      1     65      9      1      0      1      0      77     69  89% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,D796Y,N856K,Q954H,N969K,L981F] 
...V..I.D---...I-..D.LPFNKS.NARSRYHKYKHKY.K.HKF.      76      0     76      0      0      0      0      0      76     62  81% [A67V,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
F..V--I.D---...-I..DKLPFNKS.NARSRYHKYKHKY.K.HKF.      76      0      7     64      5      0      0      0      76     71  93% [L5F,A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
...V--I.D---...-I..D.LPF...........KYKHKY.K.HKF.      74      0      0     74      0      0      0      0      74     69  93% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R......D...G--............R.K........R....N....      74     18     33     23      0      0      0      0      74     36  48% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,E484K,D614G,P681R,D950N] 
.R..........G--............R.A........R....N....      73      0     71      1      1      0      0      0      73     34  46% [T19R,E156G,F157-,R158-,G181V,L452R,T478K,E484A,D614G,P681R,D950N] 
.R....I.D..HG--...V.G......R..........R....N....      72     17     55      0      0      0      0      0      72     48  66% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,R346G,L452R,T478K,D614G,P681R,D950N,D1260N] Delta+Y145H,A222V
.R....I....HG--...V........R..........R....N...L      71     16     47      2      3      0      2      1      71     24  33% [T19R,T95I,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+Y145H,A222V
.R..Y.I.....G--............R..........R....N....      70      0     68      1      1      0      0      0      70     52  74% [T19R,H69Y,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--............R..........R....N...A      70     46     21      1      0      0      2      0      70     38  54% [T19R,T95I,G142D,E156G,F157-,R158-,G181V,L452R,T478K,D614G,P681R,D950N,V1264A] 
.R.S.FI.D...G--............R..........R....N....      69     69      0      0      0      0      0      0      69     68  98% [T19R,A67S,V70F,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
...V--I.D---...-I..DKLPFNKS.NARSRYHKYKHK..K.HKF.      68      0     68      0      0      0      0      0      68     68 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,N856K,Q954H,N969K,L981F] 
.R....I....................R..........R....N....      66      0     20     20     26      0      0      0      66     25  37% [T19R,T95I,L452R,T478K,D614G,P681R,D950N] 
.R....I.D...G--............R..........H....N....      65     45      5     13      1      0      0      1      65     39  60% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681H,D950N] Delta+FurinRelated
.R....I.....G--...........VR..........R....N....      64      0     21     10     19      1     13      0      64     23  35% [T19R,T95I,E156G,F157-,R158-,G446V,L452R,T478K,D614G,P681R,D950N] Delta
.RF...I....HG--...V........R..........R....N....      63     12     51      0      0      0      0      0      63     52  82% [T19R,V36F,T95I,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
...V--I........-I..D.LPFNKS.NARSRYHKYKHKY.K.HKF.      61      0      7      9      0     45      0      0      61     42  68% [A67V,H69-,V70-,T95I,L141F,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
...V--I.D---.......DK..............KYKHKY.K.HKF.      60      0      0     60      0      0      0      0      60     58  96% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,G339D,R346K,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..D.LPFNKS.N......KYKHKY.K.HKF.      60      0      0     60      0      0      0      0      60     43  71% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R..........G--............R.......I..R....N....      59      0     40      6      0      0     13      0      59     20  33% [T19R,E156G,F157-,R158-,L452R,T478K,T547I,D614G,P681R,D950N] Delta
.R......DF..G--............R..........R....N....      59      1     31     27      0      0      0      0      59     41  69% [T19R,G142D,V143F,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--............R..........R.Y..N....      58      6     12     38      0      0      2      0      58     39  67% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D796Y,D950N] Delta
.I....I.D..HG--...V........R..........R....N....      58     58      0      0      0      0      0      0      58     58 100% [T19I,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] 
.R....I.D...G--...........SR..........R....N....      57     23     13     21      0      0      0      0      57     16  28% [T19R,T95I,G142D,E156G,F157-,R158-,G446S,L452R,T478K,D614G,P681R,D950N] Delta
.R..........G--...V.......VR..........R....N....      56      0      2      0     54      0      0      0      56     52  92% [T19R,E156G,F157-,R158-,A222V,G446V,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
.R......D...G--..S.........R..........R....N....      56     49      0      7      0      0      0      0      56     48  85% [T19R,G142D,E156G,F157-,R158-,R214S,L452R,T478K,Q613H,D614G,P681R,V772I,D950N] 
.R....N.D...G--............R..........R....N....      55      0     46      9      0      0      0      0      55     40  72% [T19R,T95N,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,G1167V] Delta
.R.S........G--............R..........R....N....      54      0     50      2      1      0      1      0      54     40  74% [T19R,A67S,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R..........G--...........VR..........R....N....      53      0     17     11      8      0     17      0      53     36  67% [T19R,E156G,F157-,R158-,G446V,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.....G--...S........R..........R....N....      53      0     51      1      1      0      0      0      53     40  75% [T19R,T95I,E156G,F157-,R158-,A222S,L452R,T478K,D614G,P681R,D950N] 
.R..Y.I.D..HG--...V........R..........R....N....      53     52      1      0      0      0      0      0      53     45  84% [T19R,H69Y,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
...V--I.D---...-I..D.LPFNKS.NARSRYHKYKHKY.K.HK..      52      0      2     50      0      0      0      0      52     48  92% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K] 
.I......D...G--............R..........R....N....      52      2     11     38      1      0      0      0      52     18  34% [T19I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
.R.V........G--...V........R..........R....N....      52      0     42      0     10      0      0      0      52     23  44% [T19R,A67V,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,Q1208H,M1237I] Delta+T95_,A222V
...V--I.D---...-I..DKLPF...RNARSRYHKYKHKY.K.HKF.      50      1     13     34      2      0      0      0      50     48  96% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,L452R,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
...........................R..........R..L.N....      49      0     49      0      0      0      0      0      49     38  77% [L452R,T478K,D614G,P681R,I850L,D950N] 
.R......D...--.............R..........R....N....      49      1      0     47      1      0      0      0      49     35  71% [T19R,G142D,E156-,F157-,L452R,T478K,D614G,P681R,D950N] 
....--I.D---...-I..D.LPFNKS.NARSRYHKYKHKY.K.HKF.      48      0      1      2     45      0      0      0      48     40  83% [H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R....I.D...G--............R.....Y....R....N....      48     26     19      2      0      0      0      1      48     36  75% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681R,D950N] Delta
.R......D...G--...........SR..........R....N....      47      6     14     26      1      0      0      0      47     33  70% [T19R,G142D,E156G,F157-,R158-,G446S,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D..HG--............R..........R....N....      47     23     19      3      2      0      0      0      47     27  57% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--...V........R.Q........R....N....      47      0     43      0      3      1      0      0      47     28  59% [T19R,R21T,G142D,E156G,F157-,R158-,A222V,L452R,T478K,E484Q,Q613H,D614G,P681R,D950N] Delta+T95_,A222V
.R....I.D...G--..........Y.R..........R....N....      47     47      0      0      0      0      0      0      47     47 100% [T19R,T95I,G142D,E156G,F157-,R158-,N440Y,L452R,T478K,D614G,P681R,D950N] Delta
.R....IAD...G--............R..........R....N....      46     44      0      2      0      0      0      0      46     33  71% [T19R,T95I,S112A,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
.R....I.D...G--............R.....S....R....N....      46     42      1      2      0      0      0      1      46     22  47% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,N501S,D614G,P681R,D950N] Delta
.R.........................R..........R.........      45      0     40      2      3      0      0      0      45     31  68% [T19R,L452R,T478K,D614G,P681R] 
.R......D...G--...V.......VR..........R....N....      45      1     10     17     16      0      1      0      45     32  71% [T19R,G142D,E156G,F157-,R158-,A222V,G446V,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
.R....I.D...G--.......L....R..........R....N....      45     32      4      9      0      0      0      0      45     18  40% [V16F,T19R,T95I,G142D,E156G,F157-,R158-,S373L,L452R,T478K,D614G,P681R,D950N] Delta
.R...F......G--............R..........R....N....      45      0     43      2      0      0      0      0      45     34  75% [T19R,V70F,E156G,F157-,R158-,L452R,T478K,K558N,D614G,P681R,D950N] 
.R....I.D...G--I...........R..........R....N....      45     42      0      3      0      0      0      0      45     40  88% [T19R,T95I,G142D,E156G,F157-,R158-,N211I,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.....G--............R..........R..L.N...L      44      0     44      0      0      0      0      0      44     39  88% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N,V1264L] Delta+V1264L
.R......DI..G--............R..........R....N....      44      4      1     39      0      0      0      0      44     23  52% [T19R,G142D,V143I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1228L] Delta
.R....I...-.G--............R..........R....N....      44      0     33      1      7      0      3      0      44     11  25% [T19R,T95I,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R.....LD.-.G--............R..........R....N....      44      0      0     44      0      0      0      0      44     36  81% [T19R,S112L,G142D,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta+S112L
.R......D...G--..HV........RI.........R....N....      44      0      0     44      0      0      0      0      44     38  86% [T19R,G142D,E156G,F157-,R158-,R214H,A222V,V289I,L452R,S477I,T478K,D614G,P681R,D950N] 
...V--I.D---...............R.......KYKHKY.K.HKF.      43      0     33     10      0      0      0      0      43     35  81% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,L452R,T478K,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.I....I.D...G--............R..........R....N....      43     15      7      2      2      0      0     17      43     36  83% [T19I,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
.R....I.DI..G--............R..........R....N....      43     36      0      7      0      0      0      0      43     27  62% [T19R,T95I,G142D,V143I,E156G,F157-,R158-,L452R,T478K,D614G,Q677H,P681R,D950N,A1016V] Delta+FurinRelated
.R.....LD...G--............R.A........R....N....      43      0      0     43      0      0      0      0      43     37  86% [T19R,S112L,G142D,E156G,F157-,R158-,L452R,T478K,E484A,D614G,P681R,D950N] 
...V--I.D---...-I..DK....KS.NARSRYHKYKHKY.K.HKF.      42      0      3     38      1      0      0      0      42     40  95% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..D.....KS.NARSRYHKYKHKY.K.HKF.      42      0     14     24      3      1      0      0      42     37  88% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R....I.....G--............RI.........R....N....      42      0     12      4     26      0      0      0      42     36  85% [T19R,T95I,E156G,F157-,R158-,L452R,S477I,T478K,D614G,P681R,D950N] Delta
.R..........G--............RN.........R....N....      42      0     32      9      1      0      0      0      42     38  90% [T19R,E156G,F157-,R158-,L452R,S477N,T478K,D614G,P681R,D950N] Delta
.K....I.D...G--............R..........R....N....      42     38      4      0      0      0      0      0      42     40  95% [T19K,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
....--....-..S............RR..........R....H....      41      6      2     33      0      0      0      0      41     41 100% [H69-,V70-,D80G,E96Q,Y144-,F157S,L244-,H245Y,R246-,S247-,Y248-,A264V,G446R,L452R,T478R,D614G,P681R,T859N,D936H,D950H,N978S] 
.R......D...G--.......L....R..........R....N....      41      5      6     29      1      0      0      0      41     21  51% [T19R,G142D,E156G,F157-,R158-,S373L,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--...........RR..........R....N....      41      1     38      0      2      0      0      0      41     13  31% [T19R,G142D,E156G,F157-,R158-,G446R,L452R,T478K,D614G,P681R,D950N,A1226V] Delta
.R..........G--.....K......R..........R....N....      41      0     35      0      6      0      0      0      41     14  34% [T19R,T29A,E156G,F157-,R158-,T250I,R346K,L452R,T478K,D614G,P681R,D950N] 
FR...I..D...G--............R..........R....N....      41      0      1     40      0      0      0      0      41     12  29% [L5F,T19R,V70I,G142D,E156G,F157-,R158-,Q414R,L452R,T478K,D614G,P681R,D950N] 
...V--I.D---...-I..DKLPF...........KYKHKY.K.HKF.      40      0      0     40      0      0      0      0      40     39  97% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R....V.D...G--............R..........R....N....      40     14      0     14      0      0      0     12      40     32  80% [T19R,T95V,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--S...........R..........R....N....      40      0      1     39      0      0      0      0      40     35  87% [T19R,T95I,G142D,E156G,F157-,R158-,N211S,L452R,T478K,D614G,P681R,D950N] Delta
.R....V.D..HG--...V........R..........R....N....      40     40      0      0      0      0      0      0      40     37  92% [T19R,T95V,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,A1078S] 
.R..R.I.D..HG--...V........R..........R....N....      40     40      0      0      0      0      0      0      40     38  95% [T19R,H69R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,T572I,D614G,P681R,D950N] Delta+Y145H,A222V
.RF...I.D..HG--...V........R..........H....N....      40     40      0      0      0      0      0      0      40     33  82% [T19R,V36F,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681H,D950N,A1078T] Delta+FurinRelated
.R.V--I.D---G--............R..........R....N....      39      7     12     10      5      0      5      0      39     21  53% [T19R,A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
FRF...I.D..HG--...V........R..........R....N....      39     38      1      0      0      0      0      0      39     29  74% [L5F,T19R,V36F,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
...V--I.D---...-I..D.LPFN...NARSRYHKYKHKY.K.HKF.      38      0      7     29      0      0      2      0      38     34  89% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
.R......D...G--.....I......R..........R....N....      38      7      3     27      0      1      0      0      38     31  81% [T19R,G142D,E156G,F157-,R158-,R346I,L452R,T478K,D614G,P681R,D950N] Delta
.R..........G--.......................R....N....      38      0     28      9      1      0      0      0      38     16  42% [T19R,E156G,F157-,R158-,T478K,D614G,P681R,D950N] 
.R....I.D..HG--...V.......SR..........R....N....      38     38      0      0      0      0      0      0      38     37  97% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,G446S,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
...V--I.D---...I-..D.LPFN.S.NARSRYHKYKHKY.K.HKF.      37      0     18     15      0      0      4      0      37     33  89% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,S371L,S373P,S375F,K417N,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
FR....I.....G--............R..........R..L.N....      37      0     37      0      0      0      0      0      37     27  72% [L5F,T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] Delta
.R....I.D..HG--...V.......VR..........R....N....      37     33      4      0      0      0      0      0      37     15  40% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,G446V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
......I.D..................R..........R....N....      36      0     35      1      0      0      0      0      36     24  66% [T95I,G142D,L452R,T478K,D614G,P681R,D950N] 
.R.V........G--............R..........R....N....      36      0     30      5      1      0      0      0      36     27  75% [T19R,A67V,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--............R.........SR....N....      36      3     26      6      0      0      0      1      36     25  69% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,N679S,P681R,D950N] Delta+FurinRelated
...V--I.D---...-I..DKLPFNKS.N......KYKHKY.K.HKF.      35      0      1     34      0      0      0      0      35     26  74% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R..........G--....S.......R..........R....N....      35      0     34      0      0      0      1      0      35     34  97% [T19R,E156G,F157-,R158-,G339S,L452R,T478K,D614G,P681R,D950N] Delta
.R....IPD...G--............R..........R....N....      35      8      2     25      0      0      0      0      35     31  88% [T19R,T95I,S112P,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
.R......D...G--...V.......SR..........R....N....      35      0      0      0     35      0      0      0      35     35 100% [T19R,G142D,E156G,F157-,R158-,A222V,G446S,L452R,T478K,D614G,P681R,D950N,M1237I] Delta+T95_,A222V
.R......D.-.G--...V........R..........R....N....      35      0      3     28      4      0      0      0      35     16  45% [T19R,G142D,Y144-,E156G,F157-,R158-,A222V,L452R,T478K,Q613H,D614G,P681R,D950N] Delta+T95_,A222V
.R......D...G--....S.......R..........R....N....      34      9     11     14      0      0      0      0      34     22  64% [T19R,G142D,E156G,F157-,R158-,G339S,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--...........VR.....T....R....N....      34      4      0      0     30      0      0      0      34     27  79% [T19R,T95I,G142D,E156G,F157-,R158-,G446V,L452R,T478K,N501T,D614G,P681R,D950N] Delta
.R....I.D.-.G--............R.Q........R....N....      34      3      0      9     22      0      0      0      34     10  29% [T19R,T95I,G142D,Y144-,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] 
...V--I.D---.......D.....KS.NARSRYHKYKHKY.K.HKF.      33      0     16     17      0      0      0      0      33     30  90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,G339D,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..D.LPF.KS...RSRYHKYKHKY.K.HKF.      33      0      0     33      0      0      0      0      33     30  90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,N440K,G446S,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R....I.D...G--.......................R....N....      33      3      8     17      5      0      0      0      33     15  45% [T19R,T95I,G142D,E156G,F157-,R158-,T478K,D614G,P681R,D950N] 
.R..........G--..L.........R..........R....N....      33      0     32      1      0      0      0      0      33     29  87% [T19R,E156G,F157-,R158-,R214L,L452R,T478K,D614G,P681R,D950N] Delta
FR....I.D..HG--...V........R........Y.R....N...L      33     31      2      0      0      0      0      0      33     31  93% [L5F,L18F,T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,H655Y,P681R,D950N,V1264L] Delta+FurinRelated
...V--I.D---...I-..................KYKHKY.K.HKF.      32      0      0     32      0      0      0      0      32     30  93% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..D.LPFNKS.NARSRYHKYKHK..K.HKF.      32      0     31      1      0      0      0      0      32     23  71% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,N856K,Q954H,N969K,L981F] 
.R......D...G--............R...............N....      32      0      9     23      0      0      0      0      32     13  40% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,D950N] 
.R..........G--............R..........R..L.N....      32      1     31      0      0      0      0      0      32     16  50% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] Delta
......................................R.........      31      0     20      0     11      0      0      0      31     17  54% [T478K,D614G,P681R] 
.R......D...G--.....S......R..........R....N....      31      0      3     27      0      0      1      0      31     19  61% [T19R,G142D,E156G,F157-,R158-,R346S,L452R,T478K,D614G,P681R,D950N] Delta
FR..........G--............R..........R.........      31      0     24      1      1      0      5      0      31     23  74% [L5F,T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
.R....I.D...G--............R..........R..L.N...L      31      6     24      0      1      0      0      0      31     19  61% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N,V1264L] Delta+V1264L
.R....I.....G--............R..........R.G..N....      31      0     31      0      0      0      0      0      31     27  87% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D796G,D950N,D1259Y] Delta
.RI.....D...G--............R..........R....N....      31     27      1      3      0      0      0      0      31     22  70% [T19R,V36I,G142D,E156G,F157-,R158-,D253G,L452R,T478K,D614G,P681R,D950N,A1078S] Delta
.R.........................R..........R..L.N....      30      0     30      0      0      0      0      0      30     19  63% [T19R,L452R,T478K,D614G,P681R,I850L,D950N] 
...V--I.D---...-I..DKLPFNKS.NARSRYHKYKH.Y.K.HKF.      30      0     28      2      0      0      0      0      30     22  73% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,D796Y,N856K,Q954H,N969K,L981F] 
.R......N...G--............R..........R....N....      30      1      0     29      0      0      0      0      30     15  50% [T19R,G142N,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--............R.Q.....I..R....N....      30      0     30      0      0      0      0      0      30     19  63% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,T547I,D614G,P681R,A845S,D950N] 
.R....I.D..HG--...V........R.Q........R....N....      30     29      1      0      0      0      0      0      30     29  96% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,E484Q,D614G,P681R,D950N] Delta+Y145H,A222V
...V--I.D---...-I..DKLPFNKS.NARSRYHKYKHKY.K.HK..      29      0      0     29      0      0      0      0      29     27  93% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K] 
.R....I.D..................R..........R..L.N....      29      0     28      0      1      0      0      0      29     16  55% [T19R,T95I,G142D,L452R,T478K,D614G,P681R,I850L,D950N] 
.R....I.D...G--............R.........YR....N....      29      4     24      0      1      0      0      0      29     20  68% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,N679Y,P681R,D950N] Delta+FurinRelated
.R......D...G--...V........R.......I..R....N...L      29      0      0     29      0      0      0      0      29     27  93% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,T547I,D614G,P681R,D950N,V1264L] Delta+V1264L
.R..--..D...G--............R..........R....N...L      29      0      0      0     29      0      0      0      29     20  68% [T19R,H69-,V70-,G142D,E156G,F157-,R158-,D215N,L452R,T478K,D614G,P681R,D950N,V1264L] 
........D..................R..........R....N....      28      0     26      1      1      0      0      0      28     13  46% [G142D,L452R,T478K,D614G,P681R,D950N] 
.I......D..........D.FPFN...NAR.RYH.YKHKY...HK..      28      0     19      0      9      0      0      0      28     28 100% [T19I,L24S,P25-,P26-,A27-,G142D,V213G,G339D,S371F,S373P,S375F,T376A,D405N,R408S,K417N,S477N,T478K,E484A,Q493R,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...V--I.D---...-I..DKLPF.KS...RSRYHKYKHKY.K.HKF.      28      0      0     28      0      0      0      0      28     26  92% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,N440K,G446S,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R....I.D...G--............R..........R.N..N....      28      3      0     25      0      0      0      0      28     28 100% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D796N,D950N] Delta
.R..........G--............R........Y.R....N....      28      0     13      8      3      0      4      0      28     16  57% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,H655Y,P681R,D950N] Delta+FurinRelated
.R......D...G--............Q..........R....N....      28      0      7     21      0      0      0      0      28     16  57% [T19R,G142D,E156G,F157-,R158-,L452Q,T478K,D614G,P681R,D950N] 
.R.....LD...G--............R..........R....N...L      28      0      0     28      0      0      0      0      28     28 100% [T19R,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+V1264L
.R....I.D...G--.S..........R..........R....N....      28      2      9     12      0      5      0      0      28     14  50% [T19R,T95I,G142D,E156G,F157-,R158-,L212S,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--...V........R..........R..L.N....      28      0     28      0      0      0      0      0      28     20  71% [T19R,T95I,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,I850L,D950N] 
.R....I.DF.HG--...V........R..........R....N....      28     28      0      0      0      0      0      0      28     28 100% [T19R,T95I,G142D,V143F,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
...V--I.D---.......D.LPFNKS.NARSRYHKYKH...K.HKF.      27      0     27      0      0      0      0      0      27     26  96% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N856K,Q954H,N969K,L981F] 
IR......D...G--............R..........R....N....      27      0      0     27      0      0      0      0      27     26  96% [L5I,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--.........N..R..........R....N....      27      2      7     18      0      0      0      0      27     16  59% [T19R,G142D,E156G,F157-,R158-,K417N,L452R,T478K,D614G,P681R,D950N] 
.R....I.D...G--............R........R.R....N....      27     24      2      1      0      0      0      0      27     20  74% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E554G,D614G,H655R,P681R,D950N,D1163Y] 
.R....I.....G--............R.Q........R.........      27      0     24      1      0      0      2      0      27     21  77% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R] 
.R......D...G--I-..........R..........R....N....      27      4     12     10      1      0      0      0      27     24  88% [T19R,G142D,E156G,F157-,R158-,N211I,L212-,L452R,T478K,D614G,P681R,D950N] Delta
......I...............................R....N....      26      0     26      0      0      0      0      0      26     12  46% [T95I,T478K,D614G,P681R,D950N] 
...V--I.D---...-I..D.LPFNKS.NARSRYH.YKHKY.K.HKF.      26      0     14     12      0      0      0      0      26     24  92% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R......D...G--.......P....R..........R....N....      26      0      8     18      0      0      0      0      26     15  57% [T19R,G142D,E156G,F157-,R158-,S373P,L452R,T478K,D614G,P681R,D950N] Delta
.R...F.LD...G--............R..........R....N....      26      1      0     25      0      0      0      0      26     17  65% [T19R,V70F,S112L,G142D,E156G,F157-,R158-,Q414K,L452R,T478K,D614G,P681R,D950N] Delta+S112L
.R........-.G--............R..........R....N....      26      0     12      2      2      0     10      0      26     12  46% [T19R,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R.V--I.....G--............R..........R....N....      26      0     17      0      6      0      3      0      26      8  30% [T19R,A67V,H69-,V70-,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
......................................R..L.N....      25      0     24      0      1      0      0      0      25     15  60% [T478K,D614G,P681R,I850L,D950N] 
.R....I.---.G--............R..........R....N....      25      1      3     20      0      0      0      1      25     19  76% [L8F,T19R,T95I,L141-,G142-,V143-,Y144-,E156G,F157-,R158-,L452R,T478K,T549S,D614G,P681R,A846S,D950N] Delta
...V--I.D---G--............R.......KYKHKY.K.HKF.      25      1     18      4      0      0      2      0      25     16  64% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,E156G,F157-,R158-,L452R,T478K,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
....--I.D---...-I..DKLPFNKS.NARSRYHKYKHKY.K.HKF.      25      0      0      0     25      0      0      0      25     24  96% [H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..D.LPFNKS.NARSRYHKYKHKY.K.HKFM      25      1     15      2      4      0      0      3      25     25 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F,V1264M] Omicron_BA.1
.R....I.D...G--............R..........R...KN....      25      0      6      0      0      0      0     19      25     19  76% [S12F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,N856K,D950N] Delta
.R..Y.......G--............R..........R....N....      25      1     22      1      0      0      1      0      25     10  40% [T19R,H69Y,E156G,F157-,R158-,L452R,T478K,D614G,P681R,G842S,D950N] Delta
.R....I.D...G--.....S......R..........R....N....      25      5     19      1      0      0      0      0      25     22  88% [T19R,T95I,G142D,E156G,F157-,R158-,R346S,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--...V........R..........R.........      25      0     10      4     11      0      0      0      25     15  60% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R] 
.R..........G--............R..........R.Y..N....      25      0      0      1      0      0     24      0      25     20  80% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D796Y,D950N] Delta
.R...II.D...G--............R..........R....N....      25     20      0      4      0      0      0      1      25     10  40% [V16F,T19R,V70I,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
.R......D...G--...V...P....R..........R....N....      25      0     25      0      0      0      0      0      25     25 100% [T19R,G142D,E156G,F157-,R158-,A222V,S373P,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
................................................      24      0     17      4      2      1      0      0      24     12  50% [] 
...V--I.D---...-I..D.LPF.KS.N......KYKHKY.K.HKF.      24      0      0     24      0      0      0      0      24     19  79% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,N440K,G446S,S477N,T478K,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R......Y...G--............R..........R....N....      24      8      6     10      0      0      0      0      24     21  87% [T19R,G142Y,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--............RG.........R....N....      24      1      5     18      0      0      0      0      24     12  50% [T19R,G142D,E156G,F157-,R158-,L452R,S477G,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--............R.........TR....N....      24     11      4      6      0      0      0      3      24     14  58% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,N679T,S680-,P681R,D950N] Delta+FurinRelated
FRF...I.D...G--............R..........R....N....      24     17      7      0      0      0      0      0      24     19  79% [L5F,T19R,V36F,T95I,D138Y,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1128I] Delta
...V--I.D---...-I..DKLPF...RNARSRYHKYKH.Y.K.HKF.      23     10      9      4      0      0      0      0      23     19  82% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,L452R,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,D796Y,N856K,Q954H,N969K,L981F] 
.R......D...G--............R..........R..L.N....      23      0     23      0      0      0      0      0      23      9  39% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] Delta
FR......D...G--...V........R..........R....N...L      23      2      0     20      1      0      0      0      23      9  39% [L5F,T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+V1264L
.R......D---G--............R..........R....N....      22      0     13      4      2      1      2      0      22     18  81% [T19R,G142D,V143-,Y144-,Y145-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---...-I..DKLPFN...NARSRYHKYKHKY.K.HKF.      22      0      2     18      2      0      0      0      22     21  95% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
...V--I.---....-I..DKLPFNKS.NARSRYHKYKHKY.K.HKF.      22      0      1     17      4      0      0      0      22     22 100% [A67V,H69-,V70-,T95I,G142-,V143-,Y144-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
.R......D...G--............RR.........R....N....      22      1     11      9      1      0      0      0      22     11  50% [T19R,G142D,E156G,F157-,R158-,L452R,S477R,T478K,D614G,P681R,D950N] Delta
.R....ILD...G--............R..........R....N....      22      3      6     13      0      0      0      0      22     15  68% [T19R,T95I,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta+S112L
.R....I.D...V--............R..........R....N....      22     12      5      5      0      0      0      0      22      9  40% [T19R,T95I,G142D,E156V,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
FR.S....D...G--............R..........R....N....      22      5      1     16      0      0      0      0      22     21  95% [L5F,T19R,A67S,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
FR....I.....G--............R..........R.........      22      0     21      1      0      0      0      0      22      9  40% [L5F,T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
.R....I.D..HG--...V........R........Y.R....N....      22     21      1      0      0      0      0      0      22     18  81% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,H655Y,P681R,D950N] Delta+FurinRelated
.R..--......G--............R..........R....N....      22      0     11     10      0      0      1      0      22      7  31% [T19R,H69-,V70-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
.I.................D.FPFNK..NAR.RYH.YKHKY...HK..      21      0     21      0      0      0      0      0      21     16  76% [T19I,L24S,P25-,P26-,A27-,V213G,G339D,S371F,S373P,S375F,T376A,D405N,R408S,K417N,N440K,S477N,T478K,E484A,Q493R,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...V--I.D---...-I..D.LPFNKS.NARSRYHK.KHKY.K.HKF.      21      0     18      3      0      0      0      0      21     12  57% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..D.LPF..S.NARSRYHKYKHKY.K.HKF.      21      0      2     19      0      0      0      0      21     17  80% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
...V--I.D---...-I..D.LPFNKS...RSRYHKYKHKY.K.HKF.      21      0      2     19      0      0      0      0      21     19  90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.---....-I..D.LPFNKS.NARSRYHKYKHKY.K.HKF.      21      0      0     21      0      0      0      0      21     21 100% [A67V,H69-,V70-,T95I,G142-,V143-,Y144-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
.R....I.D....--............R..........R....N....      21      0      1     20      0      0      0      0      21     16  76% [T19R,T95I,G142D,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
.R......D...G--........A...R..........R....N....      21      0     21      0      0      0      0      0      21     19  90% [T19R,G142D,E156G,F157-,R158-,S375A,L452R,T478K,D614G,P681R,D950N] Delta
.RF.....D...G--............R..........R....N....      21      0      3     18      0      0      0      0      21     10  47% [T19R,V36F,G142D,E156G,F157-,R158-,T299I,L452R,T478K,D614G,P681R,D950N] 
.R..........G--............R.....Y....R....N....      21      0      1      1     19      0      0      0      21     13  61% [T19R,E156G,F157-,R158-,L452R,T478K,N501Y,D614G,P681R,D950N] Delta
.R....I.D...G--E...........R..........R....N....      21      3     18      0      0      0      0      0      21     18  85% [T19R,T95I,G142D,E156G,F157-,R158-,N211E,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D..HG--...V........RN.........R....N....      21     21      0      0      0      0      0      0      21     21 100% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,S477N,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
...V--I.D---...-I..D.LPFNK..NARSRYHKYKHKY.K.HKF.      20      0      4     15      1      0      0      0      20     18  90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
.R....I.....G--............RN.........R....N....      20      0     19      1      0      0      0      0      20      8  40% [T19R,T95I,E156G,F157-,R158-,L452R,S477N,T478K,D614G,P681R,D950N] Delta
.R.........HG--............R..........R....N....      20      0     14      0      6      0      0      0      20      7  35% [T19R,Y145H,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R.....LD...G--............R..........R.........      20      0      0     20      0      0      0      0      20     17  85% [T19R,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R] 
.R....I.D..HG--............R..........R....N...L      20      8      0      0     12      0      0      0      20     11  55% [T19R,S71P,T95I,G142D,Y145H,E156G,F157-,R158-,L452R,T478K,D614G,P681R,T859N,D950N,V1264L] 
.R.....LD...G--............RN.........R....N....      20      0      1     19      0      0      0      0      20     20 100% [T19R,S112L,G142D,E156G,F157-,R158-,L452R,S477N,T478K,D614G,P681R,D950N] Delta+S112L
.R.V..I.D..HG--...V........R..........R....N....      20     14      6      0      0      0      0      0      20     15  75% [T19R,A67V,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
.I....I.D..HG--...V........R..........R....N...L      20     20      0      0      0      0      0      0      20     20 100% [L18F,T19I,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264L] 
...V--I.D---.......................KYKH...K.HKF.      19      0      0     19      0      0      0      0      19     18  94% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,T547K,D614G,H655Y,N679K,P681H,N856K,Q954H,N969K,L981F] 
...V--I.D---..............S.NARSRYHKYKHKY.K.HKF.      19      0     15      3      1      0      0      0      19     18  94% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R....I.D...G--............RR.........R....N....      19     15      2      2      0      0      0      0      19     11  57% [T19R,T95I,G142D,E156G,F157-,R158-,D228H,L452R,S477R,T478K,D614G,P681R,D950N,V1228L] Delta
.R.....LD...G--............RI.........R....N....      19      0      0     19      0      0      0      0      19     18  94% [T19R,S112L,G142D,E156G,F157-,R158-,L452R,S477I,T478K,D614G,P681R,R683Q,D950N] Delta+S112L
.R..........G--...V........R.......I..R....N....      19      0      1      0     18      0      0      0      19      9  47% [T19R,E156G,F157-,R158-,D215G,A222V,L452R,T478K,T547I,D614G,P681R,D950N] Delta+T95_,A222V
.R......DA..G--............R..........R....N....      19      0      0     18      1      0      0      0      19     18  94% [T19R,G142D,V143A,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
...........................................N....      18      0     15      3      0      0      0      0      18     12  66% [T478K,D614G,D950N] 
........D---...-I.......NKS.NARSRYHK.KHKY...HKF.      18      0      0     18      0      0      0      0      18     15  83% [G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,N679K,P681H,N764K,D796Y,Q954H,N969K,L981F] 
...V--I.D---...-I..DK.......NARSRYHKYKHKY.K.HKF.      18      0      0     18      0      0      0      0      18     17  94% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
FR....I.D...G--...V........R..........R....N....      18     15      2      1      0      0      0      0      18     15  83% [L5F,T19R,T95I,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] 
.R......D..HG--...V........R..........R....N....      18      7     11      0      0      0      0      0      18     10  55% [T19R,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
.R....I.D...G--............RT.........R....N....      18      2      0     15      1      0      0      0      18     11  61% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,S477T,T478K,D614G,P681R,D950N,K1073N] Delta
.R....I.D...G--............Q..........R....N....      18      4     13      1      0      0      0      0      18     10  55% [T19R,T95I,D138H,G142D,E156G,F157-,R158-,E180V,L452Q,T478K,D614G,P681R,D950N,I1114T] 
.R......D...G--...V........R..........R...SN....      18      0     18      0      0      0      0      0      18     17  94% [T19R,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,N856S,D950N] Delta+T95_,A222V
.R......D...G--.....G......R..........R....N....      18      0      1     17      0      0      0      0      18     10  55% [T19R,G142D,E156G,F157-,R158-,R346G,L452R,T478K,D614G,P681R,D950N] Delta
.R.S....D...G--...V........R..........R....N....      18      0     18      0      0      0      0      0      18     10  55% [V11I,T19R,A67S,G142D,E156G,F157-,R158-,A222V,S255F,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
FR....I.D...G--...........VR..........R....N....      18     10      8      0      0      0      0      0      18      9  50% [L5F,T19R,T95I,G142D,E156G,F157-,R158-,A262S,G446V,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.....G--...........VR.....T....R....N....      18      0      5      1     12      0      0      0      18      8  44% [T19R,T95I,E156G,F157-,R158-,G446V,L452R,T478K,N501T,D614G,P681R,D950N] Delta
.R......D...G--..Y.........R..........R....N....      18      0      0     18      0      0      0      0      18     17  94% [T19R,G142D,E156G,F157-,R158-,R214Y,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G----..........R..........R....N....      18     11      7      0      0      0      0      0      18      8  44% [T19R,T95I,G142D,E156G,F157-,R158-,N211-,L212-,L452R,T478K,D614G,P681R,D950N,H1101Q] Delta
........................T....K...Y..YK..........      17      0      0      0      0      0     17      0      17     11  64% [L18F,T20N,P26S,D138Y,R190S,R246G,T284I,K417T,E484K,N501Y,D614G,H655Y,N679K,T1027I,V1176F] Gamma+FurinRelated
.R....I.----G--............R..........R....N....      17     16      1      0      0      0      0      0      17     14  82% [T19R,H66R,T95I,P139-,F140-,L141-,G142-,V143-,Y144-,Y145-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,K1073T] Delta
...V--I.D---...I-..DKLPF...RNARSRYHKYKHKY.K.HKF.      17      0      0     17      0      0      0      0      17     14  82% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,R346K,S371L,S373P,S375F,L452R,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
...V..I.D---.......DKLPFNKS.NARSRYHKYKHKY.K.HKF.      17      0     17      0      0      0      0      0      17     17 100% [A67V,T95I,G142D,V143-,Y144-,Y145-,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..DK..............KYKHKY.K.HKF.      17      0      0     17      0      0      0      0      17     17 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I.......NKS.NARSRYHKYKH...K.HKF.      17      0      0     17      0      0      0      0      17     16  94% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N856K,Q954H,N969K,L981F] 
.R....I.D...G--...........RR..........R....N....      17      1      2      1     10      0      0      3      17     12  70% [T19R,T95I,G142D,E156G,F157-,R158-,G446R,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--............W..........R....N....      17     12      2      3      0      0      0      0      17     14  82% [T19R,T95I,G142D,E156G,F157-,R158-,L452W,T478K,D614G,P681R,D950N] 
.R....I.D...G--............RG.........R....N....      17      2      5      9      1      0      0      0      17      5  29% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,S477G,T478K,D614G,P681R,D950N] Delta
.R......DF..G--...V........R..........R....N....      17      0      2     15      0      0      0      0      17     10  58% [T19R,G142D,V143F,E156G,F157-,R158-,D215N,A222V,L452R,T478K,D614G,P681R,D950N,C1247S] Delta+T95_,A222V
.R....I.D...G--............R..........L....N....      17     13      0      3      1      0      0      0      17      6  35% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681L,D950N] 
....--..........................................      16      0     16      0      0      0      0      0      16     11  68% [H69-,V70-,L189F,N439K,D614G,V772I] 
...V--I.D---.......................KYKHK..K.HKF.      16      0      0     16      0      0      0      0      16     15  93% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,T547K,D614G,H655Y,N679K,P681H,N764K,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..D.LPFNKS.N.RSRYHKYKHKY.K.HKF.      16      0      8      8      0      0      0      0      16     13  81% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..DKLPF.KS.N......KYKHKY.K.HKF.      16      0      0     16      0      0      0      0      16      9  56% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,N440K,G446S,S477N,T478K,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R....A.D...G--............R..........R....N....      16      0      3     13      0      0      0      0      16     11  68% [T19R,T95A,G142D,E156G,F157-,R158-,Q173R,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--.....K......R..........R....N....      16     12      2      2      0      0      0      0      16      7  43% [T19R,T95I,G142D,E156G,F157-,R158-,R346K,L452R,T478K,D614G,P681R,D950N] Delta
.R....I....HG--...V........R..........R.........      16      0     16      0      0      0      0      0      16     13  81% [T19R,T95I,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R] 
.R....I.....G--............R.........YR....N....      16      0     16      0      0      0      0      0      16     12  75% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,N679Y,P681R,D950N,F1103L] Delta+FurinRelated
.R..--I.....G--............R..........R....N....      16      0     11      3      1      0      1      0      16      8  50% [T19R,H69-,V70-,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
FR..........G--...V........R..........R.........      16      0      2      0     14      0      0      0      16     13  81% [L5F,T19R,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R] 
.R....................................R..L.N....      15      0     15      0      0      0      0      0      15      9  60% [T19R,T478K,D614G,P681R,I850L,D950N] 
...V--I.D---...I...D.LPFNKS.NARSRYHKYKHKY.K.HKF.      15      0      0     15      0      0      0      0      15     11  73% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
...V--I.D---...-IL.D.LPFNKS.NARSRYHKYKHKY.K.HKF.      15      0      8      7      0      0      0      0      15     15 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,R214L,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
...V--..D---...-I..D.LPFNKS.NARS...KYKHKY.K.HKF.      15      0      0      0      0      0     15      0      15     14  93% [A67V,H69-,V70-,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..D.LPFNKS.NA.....KYKHKY.K.HK..      15      0      0     15      0      0      0      0      15     15 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K] 
...V--I.D---...-I..D.LPF......RSRYHKYKHKY.K.HKF.      15      0      0     15      0      0      0      0      15     13  86% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R......D...G--............R..........R...SN....      15      1      3     11      0      0      0      0      15     11  73% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,N856S,D950N] Delta
.R....I.D...G--............R.Q........R....N...L      15      0      0     13      2      0      0      0      15     13  86% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,T747I,D950N,V1264L] Delta+V1264L
.R...A..D...G--............R..........R....N....      15      1     11      3      0      0      0      0      15     10  66% [T19R,V70A,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
.R....I.D...G--............R..........R....S....      15     12      3      0      0      0      0      0      15     11  73% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950S] 
.R......D...G--............R.V........R....N....      15      0     13      2      0      0      0      0      15      7  46% [T19R,G142D,E156G,F157-,R158-,P251L,S349P,L452R,T478K,E484V,D614G,P681R,D950N] 
.R....I.D...G--...........VR.Q...T....R....N....      15      1      0      0     14      0      0      0      15     13  86% [T19R,T95I,G142D,E156G,F157-,R158-,G446V,L452R,T478K,E484Q,N501T,D614G,P681R,D950N] 
.R....I.D..HG--...V........R.......I..R....N....      15     13      2      0      0      0      0      0      15     13  86% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,T547I,D614G,P681R,D950N] Delta+Y145H,A222V
.R....I.D..HG--...V...P....R..........R....N....      15     14      1      0      0      0      0      0      15     14  93% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,R246G,S373P,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
.R....I...-.G--............R.Q........R....N....      15      1      0      0     14      0      0      0      15      4  26% [T19R,T95I,Y144-,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] 
...........................R..........R....N...L      14      0      4     10      0      0      0      0      14      7  50% [L452R,T478K,D614G,P681R,D950N,V1264L] 
....--....-......................Y....H.........      14      0      9      3      2      0      0      0      14      9  64% [H69-,V70-,Y144-,N501Y,A570D,D614G,P681H,T716I,S982A,D1118H] Alpha
...V--I.D---...-I..DKLPF..S.NARSRYHKYKHKY.K.HKF.      14      0      0     14      0      0      0      0      14     13  92% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
...V--I.D---...-I..D....NKS.NARSRYHKYKHKY.K.HKF.      14      0      6      5      1      0      2      0      14     10  71% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..DKLPF......RSRYHKYKHKY.K.HKF.      14      0      0     14      0      0      0      0      14     13  92% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R....I.D.....G............R..........R....N....      14      0     14      0      0      0      0      0      14     11  78% [T19R,T95I,G142D,R158G,L452R,T478K,D614G,P681R,D950N] 
.R....I.D...--.............R..........R....N....      14      0      1     13      0      0      0      0      14      6  42% [T19R,T95I,G142D,E156-,F157-,L452R,T478K,D614G,P681R,D950N] 
.R....I.D...G--.......P....R..........R....N....      14      3      7      4      0      0      0      0      14     10  71% [T19R,T95I,G142D,E156G,F157-,R158-,S373P,L452R,T478K,D614G,P681R,D950N] Delta
IR....I.D...G--............R..........R....N....      14     13      0      1      0      0      0      0      14     13  92% [L5I,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--............R.........SR....N....      14      2      9      3      0      0      0      0      14     11  78% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,N679S,P681R,D950N] Delta+FurinRelated
.R....I.D...G--..........K.R..........R....N....      14      2      1      0      0      0     11      0      14     12  85% [T19R,T95I,G142D,E156G,F157-,R158-,N440K,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D...G--...P........R..........R....N....      14      6      6      2      0      0      0      0      14      8  57% [T19R,T95I,G142D,E156G,F157-,R158-,A222P,L452R,T478K,D614G,P681R,D950N] 
.R....I.D...G--........F...R..........R....N....      14      3      5      2      0      0      0      4      14      5  35% [T19R,T95I,G142D,E156G,F157-,R158-,S375F,L452R,T478K,D614G,P681R,D950N] Delta
.R...I.LD...G--............R..........R....N....      14      0      0     14      0      0      0      0      14     12  85% [T19R,V70I,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta+S112L
.G......D...G--............R..........R....N....      14      5      7      2      0      0      0      0      14     11  78% [T19G,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
.R.....LD...G--............R.......I..R....N....      14      0      0     14      0      0      0      0      14      7  50% [T19R,S112L,G142D,E156G,F157-,R158-,L452R,T478K,T547I,D614G,P681R,D950N] Delta+S112L
.R....I....HG--............R..........R....N....      14      0     13      0      1      0      0      0      14     13  92% [T19R,T95I,Y145H,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R..N...D...G--............R..........R....N....      14      0      1     11      2      0      0      0      14     10  71% [T19R,H69N,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.D..HG--...VD.......R..........R....N....      14     14      0      0      0      0      0      0      14     10  71% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,G339D,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
.R....I.D...G--............R..........R..V.N....      14     14      0      0      0      0      0      0      14      7  50% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850V,D950N] Delta
.R....I.D...G--...V........R........Y.R....N....      14      0      0     14      0      0      0      0      14     10  71% [T19R,T95I,G142D,E156G,F157-,R158-,A222V,V289I,L452R,T478K,D614G,H655Y,P681R,D950N] Delta+FurinRelated
FR....I.D...G--............R.Q........R....N....      14      2      1      9      2      0      0      0      14     10  71% [L5F,T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,D950N] 
.R....I.D..HG--...V........R.......I..R....N...L      14     14      0      0      0      0      0      0      14     14 100% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,T547I,D614G,P681R,D950N,V1264L] Delta+Y145H,A222V
.R....I.D..HG--...V........R.......K..R....N...L      14     14      0      0      0      0      0      0      14     10  71% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,V327I,L452R,T478K,T547K,D614G,P681R,D950N,V1264L] Delta+Y145H,A222V
.R.........................R....................      13      0     13      0      0      0      0      0      13     12  92% [T19R,L452R,T478K,D614G] 
...V--I.D---...I-..D.....KS.NARSRYHKYKHKY.K.HKF.      13      0      3      9      0      0      1      0      13     12  92% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
F..V--I.D---...I-..D.LPFNKS.NARSRYHKYKHKY.K.HKF.      13      0      6      4      0      2      1      0      13      7  53% [L5F,A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
...V--I.D---...I-..D.FPFNKS.NAR.RYH.YKHKY...HK..      13      0      3      0      0     10      0      0      13     13 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,S371F,S373P,S375F,D405N,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K] 
...V--I.D---...-I..D.LPFNKS.NARSRYHKYKHKY...HKF.      13      0      2     11      0      0      0      0      13     11  84% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K,L981F] 
...V--I.D---...-I..D.L..NKS.NARSRYHKYKHKY.K.HKF.      13      0      0      2     11      0      0      0      13     13 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..DK...NKS.NARSRYHKYKHKY.K.HKF.      13      0      1     11      1      0      0      0      13     13 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..D......S.NARSRYHKYKHKY.K.HKF.      13      0      5      7      1      0      0      0      13     10  76% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...........................RN.........R....N....      13      0      0     13      0      0      0      0      13     12  92% [L452R,S477N,T478K,D614G,P681R,D950N] 
.R..........--.............R..........R....N....      13      0      8      5      0      0      0      0      13      6  46% [T19R,E156-,F157-,L452R,T478K,D614G,P681R,D950N] 
.R......D...G--............R.......K..R....N....      13      1      6      6      0      0      0      0      13      7  53% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,T547K,D614G,P681R,D950N] Delta
.R....I.....G--............R.A........R....N....      13      0      6      4      2      1      0      0      13      7  53% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,E484A,D614G,P681R,D950N] 
.R....I.D...G--............R...............N....      13      0      6      6      0      0      0      1      13      4  30% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,D950N] 
.R...FI.....G--............R..........R....N....      13      0     12      0      0      0      1      0      13     10  76% [T19R,V70F,T95I,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
.R....L.D...G--............R..........R....N....      13     11      2      0      0      0      0      0      13     12  92% [T19R,T95L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I.....G--............R.........SR....N....      13      0     12      1      0      0      0      0      13     12  92% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,D614G,N679S,P681R,D950N] Delta+FurinRelated
FR......D...G--............R..........R....N...L      13      0      6      3      4      0      0      0      13      5  38% [L5F,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+V1264L
.R....I.D..HG--...V........R..H.......R....N....      13     13      0      0      0      0      0      0      13     11  84% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,Q493H,D614G,P681R,D950N,M1229I] Delta+Y145H,A222V
-R......D...G--............R..........R....N....      13      0     10      0      0      0      3      0      13      8  61% [L5-,T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.R....I...............................R....N....      12      0      6      6      0      0      0      0      12      4  33% [T19R,T95I,D614G,P681R,D950N] 
...V--I.D---...I-..D...............KYKHKY.K.HKF.      12      0      0     12      0      0      0      0      12     12 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---................NARSRYHKYKHKY.K.HKF.      12      0      8      4      0      0      0      0      12     11  91% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..DKLPFNKS.NARSRYHKYKHKY...HKF.      12      0      0     12      0      0      0      0      12     11  91% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K,L981F] 
...V--I.D---...-I..D..PFNKS.NARSRYHKYKHKY.K.HKF.      12      0      0     12      0      0      0      0      12      8  66% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..................KYKHKY.K.HKF.      12      0      0     12      0      0      0      0      12     11  91% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..D.LPF....NARSRYHKYKH.Y.K.HKF.      12      0      3      9      0      0      0      0      12     11  91% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,D796Y,N856K,Q954H,N969K,L981F] 
.R......D...G--....D.......R..........R....N....      12      0      5      7      0      0      0      0      12      5  41% [T19R,G142D,E156G,F157-,R158-,G339D,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--............R.D........R....N....      12      0      3      9      0      0      0      0      12      9  75% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,E484D,D614G,P681R,D950N] 
.R...L..D...G--............R..........R....N....      12      0      1     10      1      0      0      0      12      9  75% [T19R,V70L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
.R......D...G--.........T..R..........R....N....      12      2      9      1      0      0      0      0      12     11  91% [T19R,G142D,E156G,F157-,R158-,K417T,L452R,T478K,D614G,P681R,D950N] 
.R..........G--............R..........R........L      12      0      9      0      0      0      3      0      12      5  41% [T19R,E156G,F157-,R158-,L452R,T478K,D614G,P681R,V1264L] 
.R....I.D...G--.....G......R..........R....N....      12      2      3      7      0      0      0      0      12      6  50% [T19R,T95I,G142D,E156G,F157-,R158-,R346G,L452R,T478K,T572I,D614G,P681R,D950N] Delta
.R..........G--............R.K........R....N....      12      0     11      1      0      0      0      0      12      7  58% [T19R,E156G,F157-,R158-,L452R,T478K,E484K,D614G,S640F,P681R,D950N] 
FR..Y...D...G--............R..........R....N....      12      1      0     11      0      0      0      0      12      9  75% [L5F,T19R,H69Y,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,A701V,D950N] Delta
.R....I.D...G--............R..........R....T....      12      0      0      0      0      0      0     12      12     12 100% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950T] 
.R....I.D.-.G--............R..........R..L.N....      12      1      7      0      0      0      4      0      12      7  58% [T19R,T95I,G142D,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,I850L,D950N] Delta
.R.....LD...G--...V........R..........R....N....      12      0      0     12      0      0      0      0      12      6  50% [T19R,S112L,G142D,E156G,F157-,R158-,A222V,L452R,T478K,D614G,E654V,P681R,D950N] Delta+T95_,A222V
.R..R...D...G--............R..........R....N....      12      0      1     11      0      0      0      0      12      4  33% [T19R,H69R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,L841I,D950N] Delta
.R....I.D...G--............RNQ........R....N....      12      9      3      0      0      0      0      0      12     12 100% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,S477N,T478K,E484Q,D614G,P681R,D950N] 
.R....I.D..HG--...V.......DR..........R....N....      12     12      0      0      0      0      0      0      12     11  91% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,Q414K,G446D,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
.R..........G--............R.....S....R....N....      12      0     12      0      0      0      0      0      12     12 100% [T19R,E156G,F157-,R158-,L452R,T478K,N501S,D614G,P681R,D950N] Delta
.R....I.D..HG--...V........R..........H....N...L      12     12      0      0      0      0      0      0      12     10  83% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,T299I,L452R,T478K,D614G,P681H,D950N,V1264L] Delta+FurinRelated
.R....I.D..HG--...I........R..........R....N....      12     12      0      0      0      0      0      0      12     12 100% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222I,L452R,T478K,D614G,P681R,D950N] 
...........................R...............N....      11      0      1     10      0      0      0      0      11      4  36% [L452R,T478K,D614G,D950N] 
.R....I.D---G--............R..........R....N....      11      0      9      0      2      0      0      0      11      8  72% [T19R,T95I,G142D,V143-,Y144-,Y145-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
...V--I.D---...I-..DK..............KYKHKY.K.HKF.      11      0      0     11      0      0      0      0      11      9  81% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,R346K,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...I-..DKLPFN.S.NARSRYHKYKHKY.K.HKF.      11      0      8      3      0      0      0      0      11     10  90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211I,L212-,G339D,R346K,S371L,S373P,S375F,K417N,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
...V--I.D---.............KS.NARSRYHKYKHKY.K.HKF.      11      1      2      7      0      0      1      0      11     10  90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..DK.PFNKS.NARSRYHKYKHK..K.HKF.      11      0     11      0      0      0      0      0      11     10  90% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..D.LPF.K..NARSRYHKYKHKY.K.HKF.      11      0      1      9      0      0      1      0      11      9  81% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,N440K,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
...V--I.D---...-I..DKLPFNKS.NA.....KYKHKY.K.HK..      11      0      0     11      0      0      0      0      11     11 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K] 
...V--I....D...-I..D.LPFNKS.NARSRYHKYKHKY.K.HKF.      11      0     11      0      0      0      0      0      11      9  81% [A67V,H69-,V70-,T95I,Y145D,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron_BA.1
......I.D..................R..........R..L.N....      11      0     11      0      0      0      0      0      11      5  45% [T95I,G142D,L452R,T478K,D614G,P681R,I850L,D950N] 
.R....I.....--.............R..........R....N....      11      0      6      5      0      0      0      0      11      6  54% [T19R,T95I,E156-,F157-,L452R,T478K,D614G,P681R,D950N] 
.R....I.....G--...V........R..........R.........      11      0      6      1      4      0      0      0      11      6  54% [T19R,T95I,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R] 
FR......D...G--............W..........R....N....      11      0      1     10      0      0      0      0      11     11 100% [L5F,T19R,G142D,E156G,F157-,R158-,L452W,T478K,D614G,P681R,D950N] 
.R....I.....G--............R.Q........R..L.N....      11      0     11      0      0      0      0      0      11      5  45% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,E484Q,D614G,P681R,I850L,D950N] 
.R....I.D...G--............R.....T....R....N....      11      1      7      0      2      0      1      0      11      7  63% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,N501T,D614G,P681R,D950N] Delta
.......LD...G--............R..........R....N....      11      0      0     11      0      0      0      0      11      6  54% [S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N,E1202Q] 
.R....I.D...G--............R.........KR....N....      11      0      1     10      0      0      0      0      11     10  90% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,N679K,P681R,P809S,G946R,D950N] Delta+FurinRelated
.R.V...LD...G--............R..........R....N....      11      0      0     11      0      0      0      0      11     10  90% [T19R,A67V,S112L,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta+S112L
.R....I.D...G--....D.......R..........R....N....      11      0      9      2      0      0      0      0      11      4  36% [T19R,T95I,G142D,E156G,F157-,R158-,G339D,L452R,T478K,D614G,P681R,D950N,D1259Y] Delta
FR......D...G--..L.........R..........R....N....      11      5      0      6      0      0      0      0      11      6  54% [L5F,T19R,G142D,E156G,F157-,R158-,R214L,L452R,T478K,D614G,P681R,D950N] Delta
.R...F......G--...........RR..........R....N....      11      0      0      0      0      0     11      0      11     10  90% [T19R,V70F,E156G,F157-,R158-,G446R,L452R,T478K,D614G,P681R,D950N] 
.R....I.D..HG--...V.......VR..........R....N...L      11     11      0      0      0      0      0      0      11      5  45% [T19R,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,G446V,L452R,T478K,D614G,P681R,D950N,V1264L] Delta+Y145H,A222V
FR......D.-.G--............R..........R....N....      11      2      7      2      0      0      0      0      11      8  72% [L5F,T19R,G142D,Y144-,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] Delta
.RF...I.D..HG--...V........RG.........R....N....      11     11      0      0      0      0      0      0      11     11 100% [T19R,V36F,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,S477G,T478K,D614G,P681R,D950N] Delta+Y145H,A222V
........D.............................R....N....      10      0     10      0      0      0      0      0      10      4  40% [G142D,T478K,D614G,P681R,D950N] 
...V--I.D---......................HKYKHKY.K.HKF.      10      0      0     10      0      0      0      0      10     10 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..DKLPFNK..NARSRYHKYKHKY.K.HKF.      10      0      1      9      0      0      0      0      10     10 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
...V--I.D---...-I..D.LPFNKS.NARSRY.KYKHKY.K.HKF.      10      1      6      1      1      1      0      0      10      8  80% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..D.LPFNKS.NARSRYHKYKH...K.HKF.      10      0      2      8      0      0      0      0      10      7  70% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..DKLPFNKS.NAR....KYKHKY.K.HKF.      10      0      0     10      0      0      0      0      10     10 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,S477N,T478K,E484A,Q493R,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
...V--I.D---...-I..DKLPF.K..NARSRYHKYKHKY.K.HKF.      10      0      0     10      0      0      0      0      10     10 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,N440K,S477N,T478K,E484A,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] Omicron+R346K
...V--I.D---...-I..DKLPFNKS...RSRYHKYKHKY.K.HKF.      10      0      0      9      1      0      0      0      10     10 100% [A67V,H69-,V70-,T95I,G142D,V143-,Y144-,Y145-,N211-,L212I,+214EPE,G339D,R346K,S371L,S373P,S375F,K417N,N440K,G446S,Q493R,G496S,Q498R,N501Y,Y505H,T547K,D614G,H655Y,N679K,P681H,N764K,D796Y,N856K,Q954H,N969K,L981F] 
.R.........................RN.........R....N....      10      0      0     10      0      0      0      0      10     10 100% [T19R,L452R,S477N,T478K,D614G,P681R,D950N] 
.R....I.....G--.....I......R..........R....N....      10      0      3      6      1      0      0      0      10      4  40% [T19R,T95I,E156G,F157-,R158-,R346I,L452R,T478K,D614G,P681R,D950N,K1073N] Delta
.R....I.D...G--............R.....I....R....N....      10      2      4      3      1      0      0      0      10      6  60% [T19R,T95I,G142D,E156G,F157-,R158-,L452R,T478K,N501I,D614G,P681R,D950N] Delta
.R....I.D.H.G--............R..........R....N....      10      6      1      3      0      0      0      0      10      3  30% [T19R,T95I,G142D,Y144H,E156G,F157-,R158-,L452R,T478K,D614G,S640F,P681R,D950N] Delta
.R..........G--............R.......I..R.........      10      0     10      0      0      0      0      0      10      4  40% [T19R,E156G,F157-,R158-,L452R,T478K,T547I,D614G,V622F,P681R] 
.R.S..I.....G--............R..........R....N....      10      0      1      4      5      0      0      0      10      2  20% [Q14H,T19R,A67S,T95I,E156G,F157-,R158-,F306L,L452R,T478K,D614G,P681R,D950N] Delta
.R..........G--............Q..........R....N....      10      0     10      0      0      0      0      0      10      7  70% [T19R,E156G,F157-,R158-,L452Q,T478K,D614G,P681R,D950N,H1083Y] 
.R....I.....G--............R.......I..R....N....      10      0      4      3      3      0      0      0      10      6  60% [T19R,T95I,E156G,F157-,R158-,L452R,T478K,T547I,D614G,P681R,D950N] Delta
.R......D...G--............R.G........R....N....      10      0      8      2      0      0      0      0      10      8  80% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,E484G,D614G,P681R,D950N] 
.R......D...G--............R..........R.H..N....      10      1      2      6      1      0      0      0      10      8  80% [T19R,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D796H,D950N] Delta
FR....I....HG--...V........R..........R....N....      10      0     10      0      0      0      0      0      10      8  80% [L5F,T19R,T95I,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,Q779E,D950N,P1162S] Delta+Y145H,A222V
.R....I.D...G--...........VR..........R..L.N....      10      2      8      0      0      0      0      0      10      4  40% [T19R,T95I,G142D,E156G,F157-,R158-,G446V,L452R,T478K,D614G,P681R,I850L,D950N] Delta
.R......D...G--..LV........R..........R....N....      10      0      9      1      0      0      0      0      10      5  50% [T19R,G142D,E156G,F157-,R158-,R214L,A222V,L452R,T478K,D614G,P681R,D950N,P1162S] Delta+T95_,A222V
FR...FI.D...G--............R..........R....N....      10     10      0      0      0      0      0      0      10      8  80% [L5F,T19R,V70F,T95I,G142D,E156G,F157-,R158-,L452R,T478K,D614G,P681R,D950N] 
.R.....LD...G--....S.......R..........R....N....      10      0      0     10      0      0      0      0      10      9  90% [T19R,S112L,G142D,E156G,F157-,R158-,G339S,L452R,T478K,D614G,P681R,D950N] Delta+S112L
.R....I.....G--..........K.R..........R....N....      10      0      0      0      0      0     10      0      10      8  80% [T19R,T95I,E156G,F157-,R158-,N440K,L452R,T478K,D614G,P681R,D950N] Delta
.R......D...G--...V...L...VR..........R....N....      10      0      0     10      0      0      0      0      10     10 100% [T19R,G142D,E156G,F157-,R158-,A222V,S373L,G446V,L452R,T478K,D614G,P681R,D950N] Delta+T95_,A222V
.R....I.D.-.G--............R.K........R....N....      10      1      5      2      2      0      0      0      10      9  90% [T19R,T95I,G142D,Y144-,E156G,F157-,R158-,L452R,T478K,E484K,D614G,S673T,P681R,D950N] 
.RF...I.D..HG--...V........R..........R....N...F      10     10      0      0      0      0      0      0      10     10 100% [T19R,V36F,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N,V1264F] Delta+Y145H,A222V
.R.S..I.D..HG--...V........R..........R....N....      10      3      7      0      0      0      0      0      10     10 100% [T19R,A67S,T95I,G142D,Y145H,E156G,F157-,R158-,A222V,L452R,T478K,D614G,P681R,D950N] Delta+Y145H,A222V

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last modified: Mon Jan 10 22:17 2022



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