To approximate this, each ORF assigned to a COG was weighted by the number of clones contributing to the contig and divided by the length of the contig to account for contig depth.
The average contig length of all contigs was 642 bp with contig depth of 80 reads.
Importantly, contig depth is a more important variable than contig length when estimating SNP frequencies.
These were assembled into 1,831 contigs (mean contig depth = 4.1 sequences).
Our results support the idea that SNP frequency increases with contig length and depth, but that contig depth is a much more meaningful factor in SNP discovery.
Figures 1 and 2 represent contig length and contig depth as averaged across the normalized and native libraries.
The number of contigs with or without SNPs was counted according to the number of clones within each contig, which defines the contig depth.
To improve this in SOAPdenovo2, the main changes during the scaffolding stage were as follows: 1) we detected heterozygous contig pairs using contig depth and local contig relationships.
However, no correlation between contig depth and level of SNP validation was observed.
The histogram of contig depth showed that contigs with fewer than 4 copies and singletons accounted for 87% of unique sequences.
