The presence and impact of reference bias on population genomic studies of prehistoric human populations.

ABSTRACT: Haploid high quality reference genomes are an important resource in genomic research projects. A consequence is that DNA fragments carrying the reference allele will be more likely to map successfully, or receive higher quality scores. This reference bias can have effects on downstream population genomic analysis when heterozygous sites are falsely considered homozygous for the reference allele. In palaeogenomic studies of human populations, mapping against the human reference genome is used to identify endogenous human sequences. Ancient DNA studies usually operate with low sequencing coverages and fragmentation of DNA molecules causes a large proportion of the sequenced fragments to be shorter than 50 bp-reducing the amount of accepted mismatches, and increasing the probability of multip

SUBMITTER: Gunther T 

PROVIDER: S-EPMC6685638 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature