Table 3 SNP classifications and recommendations using 622 passing samples derived from blood or cell line
From: Smokescreen: a targeted genotyping array for addiction research
| SNPolisher ConversionType | Previously validated markers | Previously failed-validation markers | De novo markers | Total SNPs | Recommendation to keep for analysis |
|---|---|---|---|---|---|
| PolyHighResolution | 441120 (68.26 %) | 17595 (2.72 %) | 7547 (1.17 %) | 466262 (72.15 %) | yes |
| NoMinorHom | 62639 (9.69 %) | 6360 (0.98 %) | 6173 (0.96 %) | 75172 (11.63 %) | yes |
| MonoHighResolution | 12095 (1.87 %) | 7061 (1.09 %) | 28614 (4.43 %) | 47770 (7.39 %) | yes if previously validated or de novo |
| Other | 6031 (0.93 %) | 14515 (2.24 %) | 27537 (4.26 %) | 48083 (7.44 %) | no |
| CallRateBelowThreshold | 3078 (0.48 %) | 2856 (0.42 %) | 1080 (0.17 %) | 7014 (1.09 %) | no |
| OTV | 370 (0.06 %) | 535 (0.08 %) | 860 (0.13 %) | 1765 (0.27 %) | yes if off-target variant genotyped |
| Hemizygous | 180 (0.03 %) | 1 (<0.01 %) | 0 (0.00 %) | 181 (0.03 %) | yes if visually inspected |
| TOTAL | 525513 (81.32 %) | 48923 (7.57 %) | 71811 (11.11 %) | 646247 |
