Figure 5.

(A) Scenario 1 of orphan read on mitochondria: one read from the pair is originally mapped to nuMTs, leaving the other read from that pair as an orphan. (B) Scenario 2 of orphan read on mitochondria: one read from the pair is originally mapped to mitochondrial sequences, but when only nuclear genome is provided during alignment, this read is forced to map to nuMTs (although this alignment is globally sub-optimal), leaving the other read from that pair as an orphan. A colour version of this figure is available at BIB online: http://bib.oxfordjournals.org.