Table 1.
Sequence read totals and consensus distribution for pure subtype samples and mixture analysis
| Sample | Region | Total no. of reads | No. of consensus sequences (≥10) | No. of plate divisions | Minor variant/no. of consensus sequences detected (≥10 reads) | % minor variant |
|---|---|---|---|---|---|---|
| A1 | p24 | 20,808 | 162 | 1 | NAa | NA |
| A2 | p24 | 21,222 | 104 | 1 | NA | NA |
| D1 | p24 | 19,596 | 163 | 1 | NA | NA |
| D2 | p24 | 17,446 | 139 | 1 | NA | NA |
| D3 | p24 | 13,137 | 73 | 4 | NA | NA |
| D4 | p24 | 11,442 | 81 | 4 | NA | NA |
| A2/D1 ratio, 50:50 | p24 | 18,702 | 146 | 1 | D1/115 | 78.8 |
| A2/D1 ratio, 95:5 | p24 | 18,694 | 133 | 1 | D1/86 | 64.7 |
| A2/D1 ratio, 99:1 | p24 | 19,216 | 117 | 1 | D1/63 | 53.8 |
| D3/A2 ratio, 99.9:0.1 | p24 | 11,299 | 70 | 4 | A2/0 | 0 |
| A1/A2 ratio, 95:5 | p24 | 18,855 | 138 | 1 | A2/20 | 14.5 |
| D1/D2 ratio, 95:5 | p24 | 17,783 | 167 | 1 | D2/0 | 0 |
| D3/D4 ratio, 95:5 | p24 | 7,461 | 44 | 4 | D4/11 | 25 |
| A3 | gp41 | 9,328 | 55 | 4 | NA | NA |
| A4 | gp41 | 7,678 | 58 | 4 | NA | NA |
| D5 | gp41 | 8,461 | 40 | 4 | NA | NA |
| D6 | gp41 | 6,310 | 47 | 4 | NA | NA |
| A4/D5 ratio, 50:50 | gp41 | 7,229 | 58 | 4 | D5/19 | 32.8 |
| A4/D5 ratio, 95:5 | gp41 | 7,561 | 51 | 4 | D5/4 | 7.8 |
| A4/D5 ratio, 99:1 | gp41 | 7,990 | 64 | 4 | D5/4 | 6.3 |
| A4/D5 ratio, 99.9:0.1 | gp41 | 7,137 | 54 | 4 | D5/1 | 1.9 |
| A3/A4 ratio, 95:5 | gp41 | 9,531 | 59 | 4 | A4/14 | 23.7 |
| D5/D6 ratio, 95:5 | gp41 | 7,532 | 59 | 4 | D6/2 | 3.4 |
a
NA, not applicable.