Massively parallel sequencing of the entire control region and targeted coding region SNPs of degraded mtDNA using a simplified library preparation method

•We propose a simplified library preparation method composed of 2-round PCR amplification.•mtDNA sequencing targeted the entire control region and 32 SNPs in the coding region.•We obtained successful NGS results for 336 fragments from 12 degraded samples.•Each sample was assigned to a certain haplogroup according to the observed sequence variation.•NGS results of the control region corresponded to those using Sanger method.