Table 2 Read codes and associated probabilities for depth of d ≥ 8 for one individual and the number of wild-type alleles specified for a folded SFS
No. of wild-type alleles in genotypeRead codeProbability
2 or 00e0 + e2/(3d)
10
3 or 6e1 + 2e2/(3d)
4 or 5(d − 1)e2/(3d)
72(d − 1)e2/(3d)
102b0e0 + 2b1e1/(3d)
12b2(d − 2)e1/(3d) + 2b3e0 + 2b3(d − 3)e1/(3d) + (1 – 2(b0 + b1 + b2 + b3))(e0 + e1/3)
3 or 62b0e1 + 2b1e0 + 4b1e1/(3d) + 4b2e1/(3d)
4 or 52b1(d − 1)e1/(3d) + 2b2e0 + 2b3e1/d
74b1(d − 1)e1/(3d) + 4b2e1/d + 4b3e1/3 + (1 – 2(b0 + b1 + b2 + b3))(2e1/3)
  • The term ex = Poisson(x, dε) is the Poisson probability of x errors, given an expected number of errors dε. The term by = bin(y, d, 0.5) is the binomial probability of observing y major type bases in a sample of d reads at a site, given that the site is heterozygous.