Over-representation analysis
The 5-mer analysis examines the enrichment of penta-nucleotides. The enrichment of 5-mers is calculated as the ratio of observed and expected 5-mer frequencies. The expected frequency is calculated as product of the empirical nucleotide probabilities that make up the 5-mer. (Example: given the 5-mer = CCCCC and cytosines have been observed to 20% in the examined sequences, the 5-mer expectation is 
). Note that 5-mers that contain ambiguous bases (anything different from A/T/C/G) are ignored.
- Individual 5-mer distribution
- Calculates the absolute coverage and enrichment for each 5-mer (observed/expected based on background distribution of nucleotides) for each base position, and plots position vs enrichment data for the top five enriched 5-mers (or fewer if less than five enriched 5-mers are present). This analysis will reveal if there is a pattern of bias at different positions over the read length. Such a bias might origin from non-trimmed adapter sequences, poly-A tails or other sources.