TABLE 2.
mtDNA variants called in CHD trio dataset by variant callers using their default parameters (1% heteroplasmy threshold for Mutserve, 5% for Mitoseek, 0 for mitoCaller, and 20% for MToolBox).
| Caller | Comparing child with parents (126 trios) | Comparing mother with father | |||||
|---|---|---|---|---|---|---|---|
| # Variants in child | # Shared with mother | # Shared with father | # Variants in mother | # Shared with father | |||
| GATK Haplotypecaller | Homoplasmy | 3,357 | 3,339 (99.46%) | 1,320 (39.32%) | 3,348 | 1,320 (39.43%) | |
| Heteroplasmy | 62 | 36 (58.06%) | 6 (9.68%) | 62 | 6 (9.68%) | ||
| mitoCaller | Homoplasmy | 2,630 | 2,297 (87.34%) | 980 (37.26%) | 2,518 | 966 (38.36%) | |
| Heteroplasmy | 5,284 | 2,315 (43.81%) | 1,905 (36.05%) | 5,551 | 1,839 (33.13%) | ||
| Mutserve | Homoplasmy | 3,112 | 2,968 (95.37%) | 1,230 (39.52%) | 3,043 | 1,227 (40.32%) | |
| Heteroplasmy | 1,099 | 485 (44.13%) | 485 (44.13%) | 1,441 | 506 (35.11%) | ||
| MitoSeek | Homoplasmy | NA | NA | NA | NA | NA | |
| Heteroplasmy | 160 | 80 (50.00%) | 52 (32.50%) | 131 | 46 (35.11%) | ||
| MToolBox | Homoplasmy | 457 | 280 (61.27%) | 11 (2.41%) | 403 | 8 (1.99%) | |
| Heteroplasmy | 661 | 517 (78.21%) | 60 (9.08%) | 701 | 64 (9.13%) | ||