Table 1.

Six informative genotype combinations to estimate heterogeneity/contamination ratio^a

Combination	1	2	3	4	5	6
S1 genotype	AA	AA	AA	AT	AT	AT
S2 genotype	TT	AT	TG	GG	AG	GC
S2 ratio (SNP heterogeneity ratio)	T/(A + T)b	2T/(A + T)b	(T + G)/(A + T + G)	G/(A + T + G)c	2G/(A + T + G)	(G + C)/(A + T + G + C)
Nucleotide frequency pattern	Large A, small T	Large A, small T	Large A, small T and G	Large A and T, small G	Large A and T, small G	Large A and T, small G and C

^aS1 is the major component and S2 is the minor/contaminating component in the mixed sample. Each combination uses specific nucleotides to represent a class of combinations; for example, the first combination denotes that both are homozygous genotypes with different nucleotides. In the formulas for calculating S2 ratio, a nucleotide denotes its count (total number of reads) in NGS sequencing data.

^bCombinations 1 and 2 cannot be distinguished from observed NGS data, so 1.5T/(A + T) is used for both.

^cCombinations 4 and 5 cannot be distinguished from observed NGS data, so 1.5G/(A + T + G) is used for both.