genotypesEstimated by EM (M-step)GiGenotype at position iEstimated by EM (E-step)aijIndicates whether read j at position i matches the referenceObserved in SNVMix1, latent in SNVMix2zijIndicates whether read j aligns to its stated positionLatentqijProbability that base call is correctObserved (SNVMix2 only)rijProbability that alignment is correctObserved (SNVMix2 only)μkParameter of the Binomial for genotype kEstimated by EM (M−step)αShape parameter of Beta prior on μ(1000,500,1)βScale parameter of Beta prior on μ(1,500,1000)
