Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding.

ABSTRACT: We describe the genome sequencing of an anonymous individual of African origin using a novel ligation-based sequencing assay that enables a unique form of error correction that improves the raw accuracy of the aligned reads to >99.9%, allowing us to accurately call SNPs with as few as two reads per allele. We collected several billion mate-paired reads yielding approximately 18x haploid coverage of aligned sequence and close to 300x clone coverage. Over 98% of the reference genome is covered with at least one uniquely placed read, and 99.65% is spanned by at least one uniquely placed mate-paired clone. We identify over 3.8 million SNPs, 19% of which are novel. Mate-paired data are used to physically resolve haplotype phases of nearly two-thirds of the genotypes obtained and produce phased

SUBMITTER: McKernan KJ 

PROVIDER: S-EPMC2752135 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature