Table 2.
MILANC rate across the genome or at loci with increased deviation in average local ancestry
| Method | Average MILANC | MILANC rate at loci with deviation in ancestry |
||
|---|---|---|---|---|
| EUR | NAM | AFR | ||
| GALA Mexican | ||||
| WINPOP | 2.9 | 4.9 (23) | 4.1 (25) | 7.5 (20) |
| LAMP-LD | 3.2 | 6.5 (12) | 4.9 (22) | 3.9 (13) |
| ALLOY | 3.0 | 5.6 (35) | 5.7 (34) | 6.9 (16) |
| PCAdmix | 17.09 | 19.0 (18) | 17.4 (17) | 21.0 (30) |
| GALA Puerto Rican | ||||
| WINPOP | 3.2 | 7.3 (6) | 4.9 (5) | 5.3 (10) |
| LAMP-LD | 2.5 | 3.6 (9) | 3.0 (10) | 3.8 (12) |
| ALLOY | 4.3 | 7.1 (23) | 6.1 (16) | 8.1 (15) |
| PCAdmix | 11.4 | 14.3 (11) | 14.1 (9) | 13.8 (23) |
Note: The number of loci with 3 or more standard deviations in local ancestry is denoted in paranthesis. We observed increased MILANC rate across all methods at loci with increased deviation in local ancestry.