Table 3.
Top mutations (>185 in count) in omicron variant as compared to the reference sequence NC_045512.2.
| annotation | protein | variant | varclass | Count | Refpos | refvar | qvar | qpos | qlength |
|---|---|---|---|---|---|---|---|---|---|
| Spike | S | A67 | deletion_frameshift | 575 | 21,762 | C | . | 21,483 | 29,387 |
| Predicted phosphoesterase, papain-like proteinase | NSP3 | A1892T | SNP | 302 | 8393 | G | A | 8124 | 29,387 |
| Transmembrane protein | NSP6 | I189V | SNP | 302 | 11,537 | A | G | 11,259 | 29,387 |
| RNA-dependent RNA polymerase, post-ribosomal frameshift | NSP12b | P314L | SNP | 302 | 14,408 | C | T | 14,130 | 29,387 |
| Spike | S | T547K | SNP | 302 | 23,202 | C | A | 22,915 | 29,387 |
| Spike | S | D614G | SNP | 302 | 23,403 | A | G | 23,116 | 29,387 |
| Spike | S | H655Y | SNP | 302 | 23,525 | C | T | 23,238 | 29,387 |
| ORF6 protein | ORF6 | M19M | SNP_silent | 302 | 27,259 | A | C | 26,972 | 29,387 |
| Predicted phosphoesterase, papain-like proteinase | NSP3 | K38R | SNP | 301 | 2832 | A | G | 2566 | 29,387 |
| Spike | S | N679K | SNP | 301 | 23,599 | T | G | 23,312 | 29,387 |
| Transmembrane protein | NSP4 | T492I | SNP | 301 | 10,029 | C | T | 9760 | 29,378 |
| Nucleocapsid protein | N | RG203K* | SNP | 301 | 28,881 | GGG | AAT | 28,806 | 29,693 |
| Growth-factor-like protein | NSP10 | V57V | SNP_silent | 300 | 13,195 | T | C | 12,917 | 29,387 |
| Spike | S | P681H | SNP | 300 | 23,604 | C | A | 23,317 | 29,387 |
| Spike | S | D796Y | SNP | 300 | 23,948 | G | T | 23,661 | 29,387 |
| Spike | S | N856K | SNP | 300 | 24,130 | C | A | 23,843 | 29,387 |
| Spike | S | Q954H | SNP | 300 | 24,424 | A | T | 24,137 | 29,387 |
| Nucleocapsid protein | N | RG203KR | SNP | 300 | 28,881 | GGG | AAC | 28,594 | 29,387 |
| RNA-dependent RNA polymerase, post-ribosomal frameshift | NSP12b | N591N | SNP_silent | 298 | 15,240 | C | T | 14,962 | 29,387 |
| Spike | S | T95I | SNP | 298 | 21,846 | C | T | 21,562 | 29,387 |
| Predicted phosphoesterase, papain-like proteinase | NSP3 | F106F | SNP_silent | 297 | 3037 | C | T | 2771 | 29,387 |
| Spike | S | G339D | SNP | 297 | 22,578 | G | A | 22,291 | 29,387 |
| ORF3a protein | ORF3a | T64T | SNP_silent | 297 | 25,584 | C | T | 25,297 | 29,387 |
| NA | 5′UTR | 241 | extragenic | 297 | 241 | C | T | 187 | 29,693 |
| 3C-like proteinase | NSP5 | P132H | SNP | 296 | 10,449 | C | A | 10,180 | 29,387 |
| 3′-to-5′ exonuclease | NSP14 | I42V | SNP | 296 | 18,163 | A | G | 17,885 | 29,387 |
| Envelope | E | T9I | SNP | 296 | 26,270 | C | T | 25,983 | 29,387 |
| ORF7b protein | ORF7b | L17L | SNP_silent | 296 | 27,807 | C | T | 27,520 | 29,387 |
| Spike | S | N969K | SNP | 294 | 24,469 | T | A | 24,182 | 29,387 |
| Predicted phosphoesterase, papain-like proteinase | NSP3 | A889A | SNP_silent | 293 | 5386 | T | G | 5120 | 29,387 |
| Spike | S | L981F | SNP | 292 | 24,503 | C | T | 24,216 | 29,387 |
| Spike | S | D1146D | SNP_silent | 292 | 25,000 | C | T | 24,713 | 29,387 |
| Membrane | M | A63T | SNP | 289 | 26,709 | G | A | 26,422 | 29,387 |
| Predicted phosphoesterase, papain-like proteinase | NSP3 | S1265 | deletion | 288 | 6513 | GTT | . | 6246 | 29,387 |
| Transmembrane protein | NSP6 | L105 | deletion | 287 | 11,286 | TGTCTGGTT | . | 11,016 | 29,387 |
| Spike | S | I68 | deletion_frameshift | 287 | 21,767 | CATG | . | 21,486 | 29,387 |
| Spike | S | E484A | SNP | 284 | 23,013 | A | C | 22,726 | 29,387 |
| Spike | S | S477N | SNP | 283 | 22,992 | G | A | 22,705 | 29,387 |
| Spike | S | T478K | SNP | 283 | 22,995 | C | A | 22,708 | 29,387 |
| Spike | S | Q493R | SNP | 282 | 23,040 | A | G | 22,753 | 29,387 |
| Spike | S | Q498R | SNP | 281 | 23,055 | A | G | 22,768 | 29,387 |
| Spike | S | N501Y | SNP | 281 | 23,063 | A | T | 22,776 | 29,387 |
| Spike | S | G496S | SNP | 280 | 23,048 | G | A | 22,761 | 29,387 |
| Spike | S | Y505H | SNP | 277 | 23,075 | T | C | 22,788 | 29,387 |
| Membrane | M | D3G | SNP | 275 | 26,530 | A | G | 26,243 | 29,387 |
| Membrane | M | Q19E | SNP | 272 | 26,577 | C | G | 26,290 | 29,387 |
| Spike | S | S371L | SNP | 270 | 22,673 | TC | CT | 22,386 | 29,387 |
| Spike | S | S373P | SNP | 270 | 22,679 | T | C | 22,392 | 29,387 |
| Spike | S | G142 | deletion | 260 | 21,987 | GTGTTTATT | . | 21,702 | 29,387 |
| Spike | S | S375F | SNP | 260 | 22,686 | C | T | 22,399 | 29,387 |
| ORF7b protein | ORF7b | E3* | SNP_stop | 253 | 27,762 | G | T | 27,687 | 29,752 |
| Spike | S | I210 | insertion_frameshift | 243 | 22,193 | . | T | 21,901 | 29,387 |
| Spike | S | R214 | insertion_frameshift | 243 | 22,203 | . | A | 21,916 | 29,387 |
| Spike | S | R214R | SNP_silent | 243 | 22,204 | T | A | 21,917 | 29,387 |
| Nucleocapsid protein | N | E31 | deletion | 243 | 28,362 | GAGAACGCA | . | 28,074 | 29,378 |
| Spike | S | L212* | SNP_stop | 243 | 22,197 | T | G | 22,118 | 29,749 |
| Spike | S | N211K | SNP | 242 | 22,195 | T | G | 21,903 | 29,387 |
| Spike | S | L212C | SNP | 242 | 22,197 | TA | GC | 21,905 | 29,387 |
| Spike | S | S214 | insertion | 242 | 22,201 | . | AGC | 21,910 | 29,387 |
| Spike | S | V213 | insertion_frameshift | 242 | 22,202 | . | A | 21,914 | 29,387 |
| NA | 3′UTR | 28,271 | extragenic | 242 | 28,271 | A | T | 27,984 | 29,378 |
| Nucleocapsid protein | N | P13L | SNP | 241 | 28,311 | C | T | 28,024 | 29,378 |
| Spike | S | N764K | SNP | 234 | 23,854 | C | A | 23,567 | 29,387 |
| Spike | S | G446S | SNP | 203 | 22,898 | G | A | 22,611 | 29,387 |
| Spike | S | N440K | SNP | 199 | 22,882 | T | G | 22,595 | 29,387 |
| Spike | S | K417N | SNP | 183 | 22,813 | G | T | 22,526 | 29,387 |