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Illumina reads, despite being much shorter, provide a higher depth of coverage than 454 reads.
For WGS and exome data, high sensitivity and specificity could also be achieved, but only at much higher depth of coverage.
Since these haplotyped SNPs are inherited as a block, future studies would benefit from a higher depth of coverage to ensure complete linkage of haplotype blocks.
We showed that a relatively higher depth of coverage (more than 20×) was required to gain good performance in SV detection from simulation experiments.
Lr1 gave a higher depth of coverage than expected (7× rather than 2-3×), indicathat therethere may be 2 or 3 genes with highly similar sequences on this chromosome arm.
All intervals having at least six out of seven consecutive windows with a significantly higher depth of coverage (number of reads greater than or equal to the average plus 3 standard deviations) were considered SDs.
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Fifty-fold coverage is also sufficient to identify nearly all of the insertions and deletions observed at higher depths of coverage.
SNPs identified uniquely at higher depths of coverage include variants in regions where the average base quality is low, regions with unusually low depths of coverage compared to the rest of the genome, and regions with false positive calls due to misalignment of reads across a deletion.
The designs of NGS having a high depth of coverage and robust analytical pipelines can lead to the successful detection of a wide range of genomic defects in PCC/PGL.
The Illumina sequence reads are likely to represent the entire genomes of E-Pae and I-Pae given their high depth of coverage.
In studies with a high depth of coverage it is the sequencing error rate (both sequencing and PCR errors) that is the limiting factor in the identification of very rare variants.
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