Table B2 . The hidden states of the HMM, their biological interpretation, and the mean and variance parameters used for the negative binomially distributed emission probabilities of observed read count.

Hidden state (copy no.)	Emission probability	Description
1	NB(λ, ηλ)	Normal (euploid)
0	NB(ελ, εηλ)	Deletion
2	NB(2λ, 2ηλ)	Duplication
3	NB(3λ, 3ηλ)	High copy no.