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HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph

Fig 8

Illustration of P[b_i,j|h_k].

Probability of observing a given nucleobase under the hypothesis that the sample belongs to a particular haplogroup. The rectangular box is the observed base. The probability of no mutation is 1 − π, and the remaining probability mass is distributed with reference to the of human mtDNA. Transitions are shown in green, transversions in blue. We assign probability 1 − ϵ to the event that no sequencing error has occurred. The remaining probability mass is equidistributed across the other three bases which may be the underlying base in the sample. Not all arrows are shown.

doi: https://doi.org/10.1371/journal.pcbi.1011148.g008