Table 2. Alternative SNPs and their effect on protein coding.
| Primer ID | Gene | Protein | Position | Alternative Codons | Syn. / Non-syn. | Alternative amino acids | ||
|---|---|---|---|---|---|---|---|---|
| Bris_SARS-CoV-2_313 | ORF1a | Nsp2 | 3 | CTC | CTT | Syn | Leucine | ---- |
| Bris_SARS-CoV-2_1059 | ORF1a | Nsp2 | 2 | ACC | ATC | Syn | Threonine | ---- |
| Bris_SARS-CoV-2_2416 | ORF1a | Nsp3 | 3 | TAC | TAT | Syn | Threonine | ---- |
| Bris_SARS-CoV-2_2558 | ORF1a | Nsp3 | 1 | CCA | TCA | Non | Proline | Serine |
| Bris_SARS-CoV-2_2891 | ORF1a | Nsp3 | 1 | GCA | ACA | Non | Alanine | Threonine |
| Bris_SARS-CoV-2_4002 | ORF1a | Nsp3 | 2 | ACT | ATT | Non | Threonine | Isoleucine |
| Bris_SARS-CoV-2_11083 | ORF1a | Nsp5 | 3 | TTT | TTG | Non | Phenylalanine | Leucine |
| Bris_SARS-CoV-2_14408 | ORF1ab | Nsp12 | 2 | CTT | CCT | Non | Leucine | Proline |
| Bris_SARS-CoV-2_14805 | ORF1ab | Nsp12 | 3 | TAC | TAT | Syn | Tyrosine | ---- |
| Bris_SARS-CoV-2_17247 | ORF1ab | Nsp13 | 3 | CGT | CGC | Syn | Arginine | ---- |
| Bris_SARS-CoV-2_19839 | ORF1ab | Nsp15 | 3 | AAC | AAT | Syn | Asparagine | ---- |
| Bris_SARS-CoV-2_20268 | ORF1ab | Nsp15 | 3 | TTA | TTG | Syn | Leucine | ---- |
| Bris_SARS-CoV-2_20578 | ORF1ab | Nsp15 | 1 | GTG | TTG | Non | Valine | Leucine |
| Bris_SARS-CoV-2_25350 | S | Spike | 2 | CCA | CTA | Non | Proline | Leucine |
| Bris_SARS-CoV-2_25429 | ORF3a | Ap3a | 1 | GTA | TTA | Non | Valine | Leucine |
| Bris_SARS-CoV-2_25563 | ORF3a | Ap3a | 3 | CAG | CAT | Non | Glutamine | Histidine |
| Bris_SARS-CoV-2_27046 | M | Matrix | 2 | ACG | ATG | Non | Threonine | Methionine |
| Bris_SARS-CoV-2_28144 | ORF8 | Ap8 | 2 | TTA | TCA | Non | Leucine | Serine |
| Bris_SARS-CoV-2_28580 | N | Nucleoprotein | 1 | GAT | TAT | Non | Aspartate | Tyrosine |
In the Alternative Codons columns, the codon with the predominant SNP in the COG-UK 2020-05-08 dataset is listed first. Position refers to the SNP position with respect to the in-frame codon. Abbreviations: Nsp = non-structural protein; Ap = accessory protein; Non = non-synonymous, Syn = synonymous.