Skip to main content
. 2020 Nov 5;112(6):5331–5342. doi: 10.1016/j.ygeno.2020.11.003

Table 1.

Locus-wise distribution of the total 20,163 instances of polymorphism detected in the SARS-CoV-2 pan-genome based on 71,703 complete whole-genomes sequenced globally until 21 August 2020.

Locus (length in bp) Number of transitions detected (Ts)
 ΣTs Number of transversions detected (Tv)
 ΣTv Σ (Ts + Tv) Point mutation frequency (Mf) No. of missense mutations No. of synonymous mutations dN/dS
A➔G G➔A C➔U U➔C A➔U U➔A C➔A A➔C C➔G G➔C G➔U U➔G
5’ UTR (265) 31 33 47 35 146 21 17 15 11 8 10 30 10 122 268 1.41 × 10−5 NA NA NA
nsp1 (541) 57 79 81 68 285 20 25 14 7 4 9 54 15 148 433 1.12 × 10−5 271 155 0.7398
nsp2 (1914) 253 219 294 215 981 52 67 75 82 7 12 156 52 503 1484 1.08 × 10−5 996 477 0.9479
nsp3 (5836) 707 477 718 632 2534 154 169 175 200 34 53 388 124 1297 3831 9.15 × 10−6 2448 1351 0.5803
nsp4 (1500) 146 107 191 178 622 36 45 40 19 4 16 69 37 266 888 8.25 × 10−6 521 360 0.5126
nsp5 (918) 86 52 112 97 347 16 24 21 23 1 6 50 17 158 505 7.67 × 10−6 310 190 0.6417
nsp6 (870) 83 67 103 104 357 23 28 24 13 7 15 65 24 199 556 8.91 × 10−6 337 210 0.7000
nsp7 (249) 29 16 35 23 103 4 8 8 7 3 2 14 8 54 157 8.79 × 10−6 86 70 0.4999
nsp8 (594) 58 45 71 59 233 12 12 8 15 2 4 33 8 94 327 7.67 × 10−6 187 132 0.4892
nsp9 (339) 34 30 48 26 138 5 7 13 5 0 2 17 10 59 197 8.10 × 10−6 108 88 0.4933
nsp10 (417) 31 19 51 45 146 8 7 12 8 3 5 18 8 69 215 7.19 × 10−6 119 94 0.4187
nsp11 (39) 2 4 5 3 14 1 2 0 1 2 1 3 0 10 24 8.58 × 10−6 19 5 1.132
nsp12 (2847) 259 175 319 285 1038 55 65 54 53 13 20 219 44 523 1561 7.64 × 10−6 906 637 0.6057
nsp13 (1713) 181 96 200 173 650 37 39 53 33 6 12 133 29 342 992 8.08 × 10−6 583 405 0.4500
nsp14 (1581) 140 107 198 172 617 24 38 32 49 10 15 133 33 334 951 8.39 × 10−6 568 373 0.4024
nsp15 (1038) 149 96 112 110 467 38 30 32 39 4 21 94 21 279 746 1.00 × 10−5 514 228 0.3937
nsp16 (894) 88 68 90 106 352 29 19 23 20 7 7 70 23 198 550 8.58 × 10−6 342 200 0.4554
geneS (3822) 346 246 428 417 1437 173 107 141 117 47 122 309 103 1119 2556 9.32 × 10−6 1615 906 0.6193
orf3a (828) 89 86 137 114 426 42 38 55 40 15 36 117 35 378 804 1.35 × 10−5 588 195 1.5013
gap 2 1 2 1 6 1 0 0 1 0 0 0 0 2 8 ND NA NA NA
geneE (228) 15 19 30 32 96 8 10 12 6 8 6 24 6 80 176 1.08 × 10−5 110 63 1.0206
gap 4 1 4 9 18 3 1 0 0 2 1 5 1 13 31 ND NA NA NA
geneM (669) 50 40 82 60 232 22 14 21 11 7 17 55 18 165 397 8.28 × 10−6 209 183 0.6548
gap 1 1 0 0 2 1 1 0 1 0 0 0 0 3 5 ND NA NA NA
orf6 (186) 22 11 19 35 87 15 7 8 4 1 5 19 5 64 151 1.13 × 10−5 99 46 1.3944
gap 2 0 1 0 3 0 0 0 1 0 1 0 0 2 5 ND NA NA NA
orf7a (366) 44 30 65 54 193 23 22 20 17 12 13 47 12 166 359 1.37 × 10−5 241 95 1.1946
gap 15 11 22 25 73 6 10 1 4 0 6 15 6 48 121 ND NA NA NA
orf8 (366) 40 32 46 63 181 22 14 22 10 8 19 51 13 159 340 1.30 × 10−5 228 92 1.4522
gap 2 0 1 0 3 0 0 1 1 0 1 1 0 4 7 ND NA NA NA
geneN (1260) 160 142 215 102 619 92 33 65 52 30 58 169 24 523 1142 1.26 × 10−5 763 366 1.2633
gap 1 3 6 0 10 1 0 4 0 0 1 4 0 10 20 ND NA NA NA
orf10 (117) 10 8 16 14 48 6 3 1 3 2 3 9 2 29 77 9.18 × 10−6 53 19 1.2981
3’ UTR (229) 37 29 34 30 130 19 15 17 12 9 21 43 13 149 279 1.70 × 10−5 NA NA NA
Pan-genome (29903) 3174 2350 3783 3287 12,594 969 877 967 865 256 520 2414 701 7569 20,163 9.4 × 10−6 12,221 6940 NA

ND = not determined.

NA = not applicable.

dN = rate of missense (non-synonymous) mutation accumulation (ratio between the number of non-synonymous mutations and non-synonymous sites).

dS = rate of synonymous mutation accumulation (ratio between the number of synonymous mutations and synonymous sites).