Additional file 10: Figure S7. of Improvement in detection of minor alleles in next generation sequencing by base quality recalibration

The cumulative Ti/Tv ratio for minor alleles in mtDNA, ordered according to decreasing LLR. The first 3,000 minor alleles have a Ti/Tv >30, then the ratio decreases to and stabilizes around 18 for the next 5,000 to 30,000 minor alleles. The high Ti/Tv ratio suggests these minor alleles are probably true but have different sources: those with the highest Ti/Tv ratio are from heteroplasmy, which reflects recent mutations, while the rest probably stem from cross contamination or nuMTs, which diverged from the major allele thousands to millions years ago and hence would have a relatively lower Ti/Tv ratio. (PDF 125 kb)