Just saw this paper Sequencing and analysis of an Irish human genome. AFAIK WGS is usually done at 30x coverage. In this paper, the authors “describe a novel method for improving SNP calling accuracy at low genome coverage using haplotype information.” I thought it was pretty good considering that they had 99.3% of the reference genome covered for 10.6x coverage. That leaves only like 21 Mbases missing ..
For those interested in the tech details
Four single-end and five paired-end DNA libraries were generated and sequenced using a GAII Illumina Genome Analyzer. The read lengths of the single-end libraries were 36, 42, 45 and 100 bp and those of the paired end were 36, 40, 76, and 80 bp, with the span sizes of the paired-end libraries ranging from 300 to 550 bp (± 35 bp). In total, 32.9 gigabases of sequence were generated (Table 1). Ninety-one percent of the reads mapped to a unique position in the reference genome (build 36.1) and in total 99.3% of the bases in the reference genome were covered by at least one read, resulting in an average 10.6-fold coverage of the genome.
At 11-fold genome coverage, approximately 99.3% of the reference genome was covered and more than 3 million SNPs were detected, of which 13% were novel and may include specific markers of Irish ancestry.