Table 2.
Genotype estimates by GtTR on Illumina WGS data compared with PCR sizing analysis
| Sample (Coverage) | Methoda | Target_ID | Correlation | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| VNTR_8 | VNTR_32 | VNTR_57 | VNTR_86 | VNTR_87 | VNTR_93 | VNTR_109 | VNTR_112 | VNTR_120 | |||
| NA12877 (30X) | PCR | 12.5 | 21.8 | 12.1 | 2.0 | 7.0 | 2.0 | 16.0 | 3.4 | 2.0 | 0.9827 |
| Illumina_WGS | 10.6 | 26.6 | 13.1 | 3.0 | 6.5 | 2.1 | 19.6 | 3.1 | 2.6 | ||
| 95% HPD interval | (7.94–13.2) | (16.5–36.8) | (9.99–16.2) | (2.12–3.95) | (4.88–8.03) | (1.47–2.8) | (15–24.2) | (1.89–4.29) | (0.784–4.46) | ||
| NA12877 (200X) | PCR | 12.5 | 21.8 | 12.1 | 2.0 | 7.0 | 2.0 | 16.0 | 3.4 | 2.0 | 0.9756 |
| Illumina_WGS | 12.4 | 29.2 | 13.2 | 2.5 | 7.0 | 2.3 | 15.5 | 3.2 | 3.0 | ||
| 95% HPD interval | (10.6–14.3) | (22.4–35.9) | (11.2–15.2) | (2–3.05) | (5.89–8.03) | (1.84–2.72) | (12.9–18.1) | (2.32–3.99) | (1.73–4.24) | ||
| NA12878 (30X) | PCR | 12.0 | 9.5 | 11.6 | 2.0 | 7.5 | 2.0 | 16.0 | 3.4 | 2.0 | 0.9251 |
| Illumina_WGS | 12.0 | 17.2 | 11.2 | 2.3 | 7.5 | 2.1 | 21.5 | 3.6 | 3.8 | ||
| 95% HPD interval | (9.24–14.8) | (8.72–25.6) | (8.24–14.1) | (1.51–3.06) | (5.74–9.25) | (1.42–2.76) | (16.7–26.4) | (2.18–5.11) | (1.51–6.16) | ||
| PacBio WGS b | 12.0 | 11.9 | 11.6 | 2.5 | 7.5 | 2.0 | 16.3 | 3.5 | 3.2 | ||
| NA12879 (30X) | PCR | 12.5 | 9.8 | 10.5 | 2.0 | 8.5 | 2.0 | 16.0 | 2.9 | 2.0 | 0.9659 |
| Illumina_WGS | 11.9 | 11.4 | 12.3 | 2.2 | 9.6 | 2.2 | 23.2 | 2.1 | 3.2 | ||
| 95% HPD interval | (9.06–14.7) | (4.59–18.1) | (9.26–15.4) | (1.48–2.96) | (7.53–11.7) | (1.51–2.79) | (18.2–28.2) | (1.08–3.04) | (1.08–5.31) | ||
| NA12889 (30X) | PCR | 12.0 | 22.3 | 15.6 | 2.0 | 8.0 | 2.0 | 16.9 | 3.9 | 2.0 | 0.9883 |
| Illumina_WGS | 11.1 | 25.3 | 18.1 | 2.6 | 7.7 | 2.2 | 21.4 | 3.8 | 3.3 | ||
| 95% HPD interval | (8.47–13.7) | (16–34.5) | (14.4–21.9) | (1.78–3.34) | (5.96–9.37) | (1.55–2.89) | (16.8–26) | (2.37–5.12) | (1.32–5.31) | ||
| NA12890 (30X) | PCR | 12.5 | 9.7 | 10.5 | 2.0 | 7.5 | 2.0 | 15.1 | 2.9 | 2.0 | 0.9640 |
| Illumina_WGS | 12.7 | 10.9 | 11.0 | 2.6 | 8.2 | 1.8 | 22.0 | 2.8 | 3.3 | ||
| 95% HPD interval | (9.66–15.8) | (3.96–17.9) | (7.92–14) | (1.72–3.51) | (6.34–10.1) | (1.15–2.47) | (16.9–27) | (1.56–4.02) | (1.05–5.48) | ||
| NA12891 (30X) | PCR | 12.5 | 9.3 | 10.6 | 2.0 | 7.0 | 2.0 | 15.1 | 2.9 | 2.0 | 0.9570 |
| Illumina_WGS | 12.6 | 9.8 | 12.6 | 2.5 | 7.4 | 2.1 | 23.0 | 2.2 | 3.5 | ||
| 95% HPD interval | (9.71–15.5) | (3.2–16.4) | (9.43–15.7) | (1.66–3.3) | (5.63–9.1) | (1.42–2.74) | (17.8–28.2) | (1.17–3.27) | (1.29–5.72) | ||
| NA12892 (30X) | PCR | 12.5 | 9.8 | 12.6 | 2.0 | 9.0 | 2.0 | 16.9 | 3.9 | 2.0 | 0.9704 |
| Illumina_WGS | 12.4 | 11.4 | 15.6 | 2.6 | 9.0 | 2.1 | 24.6 | 3.1 | 2.6 | ||
| 95% HPD interval | (9.64–15.2) | (4.83–18) | (12.2–18.9) | (1.78–3.44) | (7.12–11) | (1.39–2.8) | (19.5–29.8) | (1.88–4.29) | (0.691–4.45) | ||
aValues for ‘PCR’ refers to the average number of repeats from the two alleles and the values for ‘Capture-Seq’ refers to the genotype estimates determined by the GtTR algorithm
bGenotype estimates from PacBio WGS on NA12878 sample included for comparison