Table 1.
Samples for which the SARS-CoV-2 sequence could be called at 90% of sites between 21,570 and 29,550, and the substitutions in this region relative to the putative SARS-CoV-2 progenitor proCoV2 inferred by Kumar et al. (2021).
| Sample | Fraction sites called (21,570–29,550) | Patient group | Substitutions relative to proCoV2 |
|---|---|---|---|
| A4 | 0.9266 | Early outpatient | None |
| C1 | 0.9396 | Early outpatient | G22081A (A = 924, C = 4, G = 9), C28144T (C = 6, T = 1185), T29483G (C = 1, G = 45, T = 1) |
| C2 | 0.9397 | Early outpatient | C29095T (C = 1, G = 1, T = 751) |
| C9 | 0.9005 | Early outpatient | C28144T (C = 3, T = 823), G28514T (G = 1, T = 36) |
| D9 | 0.9051 | Early outpatient | C28144T (C = 4, T = 1653) |
| D12 | 0.9400 | Early outpatient | C28144T (C = 8, T = 2400) |
| E1 | 0.9223 | Early outpatient | C28144T (T = 125) |
| E5 | 0.9227 | Early outpatient | C24034T (A = 5, C = 3, T = 74), T26729C (C = 12), G28077C (C = 142, G = 4) |
| E11 | 0.9321 | Early outpatient | C25460T (C = 2, T = 246), C28144T (C = 1, T = 412) |
| F11 | 0.9054 | Early outpatient | T25304A (A = 9, T = 1), C28144T (C = 6, G = 1, T = 1328) |
| G1 | 0.9396 | Early outpatient | None |
| G11 | 0.9112 | Early outpatient | None |
| H9 | 0.9381 | Early outpatient | C28144T (C = 2, T = 1254) |
| R11 | 0.9422 | Hospital patient (Feb) | C21707T (T = 401), C28144T (A = 1, C = 18, T = 4265) |
Numbers in parentheses after each substitution give the deep sequencing reads with each nucleotide identity.