Table 3. Comparison of genotyping and sequencing data obtained for the test set.
| Probe ID | wt Liverpool_strain | BetaCoV/England mix | Notes | COG-UK | ||
|---|---|---|---|---|---|---|
| Genotype | Sequence | Genotype | Sequence | |||
| Bris_SARS-CoV-2_313 | C:C | C | C:C | C | Concord | C/T |
| Bris_SARS-CoV-2_1059 | C:C | C | C:C | C | Concord | C/T |
| Bris_SARS-CoV-2_2416 | C:C | C | C:C | C | Concord | C/T |
| Bris_SARS-CoV-2_2558 | C:C | C | C:C | C | Concord | C/T |
| Bris_SARS-CoV-2_2891 | G:G | G | G:G | G | Concord | G/A |
| Bris_SARS-CoV-2_4002 | C:C | C | C:C | C | Concord | C/T |
| Bris_SARS-CoV-2_11083 | T:T | T | G:G | G | Separation | G/T |
| Bris_SARS-CoV-2_14408 | C:C | C | C:C | C | Concord | T/C |
| Bris_SARS-CoV-2_14805 | C:C | C | C:C | C | Concord | C/T |
| Bris_SARS-CoV-2_17247 | T:T | T | T:T | T | Concord | T/C |
| Bris_SARS-CoV-2_19839 | T:T | T | T:T | T | Concord | T/C |
| Bris_SARS-CoV-2_20268 | A:A | A | A:A | A | Concord | A/G |
| Bris_SARS-CoV-2_20578 | G:G | G | G:G | G | Concord | G/T |
| Bris_SARS-CoV-2_25350 | C:C | C | C:C | C | Concord | C/T |
| Bris_SARS-CoV-2_25429 | G:G | G | G:G | G | Concord | G/T |
| Bris_SARS-CoV-2_25563 | G:G | G | G:G | G | Concord | G/T |
| Bris_SARS-CoV-2_27046 | C:C | C | C:C | C | Concord | C/T |
| Bris_SARS-CoV-2_28144 | T:T | T | C:C | C | Separation | T/C |
| Bris_SARS-CoV-2_28580 | G:G | G | G:G | G | Concord | G/T |
Sequences “Concord” where the SARS-CoV-2 isolates GBR/Liverpool_strain/2020 and hCoV-19/England/02/2020 all share the same genotype and sequence. Separation denotes genotyping call differences between the two isolates confirmed by sequencing. Alleles in the last column are those reported in the COG-UK database (from the 2020-05-08 dataset COG consortium https://www.cogconsortium.uk/data/ (14,277 sequences) with the major/minor alleles.