Outcomes:Sucessfully aligned 33% and 21% of the SOLiD reads derived from the APG-1 and APG-2 personal genomes onto the reference human genome, respectively.
A total of 919,460 and 1,246,395 candidate variants were identified in APG-1 and APG-2 respectively.
However, APG-1 contained a greater number of variants with a quality score >= 20, most likely reflective of the greater read depth in the APG-1 alignment compared to the APG-2 alignment.
Putative Y- chromosome ancestries for both APG-1 and APG-2 were defined.
Limitations:Normally, whole genome sequencing of humans encode ~ 3 million SNPS and 300- 400k INDELS per individual.
This study only identified a subset of variations for both personal genomes owing to the limited mapping success rate of SOLiD reads onto the human reference genome.
There is a notable lack of open-source tools for quality curation, mapping and variant calling as compared to other sequencing platforms.