Table 2.

Calculation of the level of contamination by the contaminant

Observed AR of an SNP of sample A (AR(A))	AR of the same SNP of contaminant B	Calculation of the percentage of contaminant DNA (B) in sample (A) for each SNP
0–0.25	0.25–0.75	(0 + AR(A))×2
0–0.25	0.75–1	(0 + AR(A))
0.75–1	0.25–0.75	(1−AR(A))×2
0.75–1	0–0.25	(1−AR(A))

After identifying the contaminant, for each homozygous SNP, the difference between the theoretical AR (0 for Ref/Ref, 1 for Alt/Alt) and the observed AR (column 1) is used to calculate the contamination percentage (column 3) according to the genotype of the contaminant (column 2)