Table 2 Effect of read length and base error on HLAminer predictions from targeted assembly of simulated RNA-Seq dataa
From: Derivation of HLA types from shotgun sequence datasets
HLA allele resolution | Base error (%) | Read length (nucleotides) | Sensitivity (mean ± SD%) | Specificity (mean ± SD%) | Ambiguity(mean ± SD%) |
|---|---|---|---|---|---|
Two-digit | 1.0 | 50 | 13.62 ± 2.80 | 92.86 ± 10.10 | 19.06 ± 16.53 |
|  |  | 75 | 62.32 ± 3.62 | 90.27 ± 3.28 | 8.93 ± 2.67 |
|  |  | 100 | 95.72 ± 0.53 | 96.31 ± 0.02 | 4.46 ± 3.84 |
|  |  | 150 | 97.97 ± 2.80 | 95.73 ± 3.63 | 0.00 ± 0.00 |
Two-digit | 0.5 | 100 | 93.04 ± 4.60 | 96.39 ± 1.44 | 2.91 ± 1.69 |
|  | 1.0 |  | 95.72 ± 0.53 | 96.31 ± 0.02 | 4.46 ± 3.84 |
|  | 2.0 |  | 64.64 ± 4.79 | 96.13 ± 1.43 | 13.40 ± 3.02 |
|  | 3.0 |  | 6.67 ± 2.51 | 100.00 ± 0.00 | 8.59 ± 8.34 |
Four-digit | 1.0 | 50 | 7.78 ± 1.92 | 60.51 ± 20.02 | 27.78 ± 4.81 |
|  |  | 75 | 51.94 ± 2.93 | 77.36 ± 5.44 | 37.38 ± 11.16 |
|  |  | 100 | 86.84 ± 1.75 | 88.13 ± 1.41 | 36.32 ± 4.76 |
|  |  | 150 | 93.33 ± 3.63 | 93.07 ± 2.91 | 22.87 ± 2.40 |
Four-digit | 0.5 | 100 | 84.72 ± 5.42 | 89.65 ± 2.25 | 24.03 ± 3.00 |
|  | 1.0 |  | 86.84 ± 1.75 | 88.13 ± 1.41 | 36.32 ± 4.76 |
|  | 2.0 |  | 56.94 ± 1.73 | 87.49 ± 4.77 | 39.14 ± 5.73 |
|  | 3.0 |  | 4.44 ± 2.10 | 68.69 ± 17.03 | 37.22 ± 25.62 |