Table 3. Non-reference MEI genotype contingency tables.

Low coverage pilot					Trio pilot
		PCR genotypes					PCR genotypes
Sequenced genotypes		0/0	0/1	1/1	Sequenced genotypes		0/0	0/1	1/1
	0/0	2773	188	5		0/0	901	5	0
	0/1	18	913	217		0/1	2	671	54
	1/1	1	140	372		1/1	0	10	144

Low coverage pilot samples; trio pilot samples. Genotypes are listed in “VCF” convention: 0/0 homozygous reference, 0/1 heterozygous MEI, 1/1 homozygous MEI. For the low coverage validation, 23 samples at 333 sites were tested, while for the trio data all 6 samples were tested at 332 sites. The agreement for the low coverage data is 88.7% with 58% of the sites genotyped with GQ≥7. Genotype agreement for the pilot data was 96% with 90% genotyping efficiency.