Per-base analysis
- Coverage
- Calculates absolute coverages for individual base positions. The resulting graph correlates base-positions with the number of sequences that supported (covered) that position.
- Nucleotide contributions
- Calculates absolute coverages for the four DNA nucleotides (A, C, G or T) for each base position in the sequences. In a random library you would expect little or no difference between the bases, thus the lines in this plot should be parallel to each other. The relative amounts of each base should reflect the overall amount of the bases in your genome. A strong bias along the read length where the lines fluctuate a lot for certain positions may indicate that an over-represented sequence is contaminating your sequences. However, if this is at the 5' or 3' ends, it will likely be adapters that you can remove using the Trim Reads tool.
- GC-content
- Calculates absolute coverages of C's + G's for each base position in the sequences. If you see a GC bias with changes at specific base positions along the read length this could indicate that an over-represented sequence is contaminating your library.
- Ambiguous base-content
- Calculates absolute coverages of N's, for each base position in the sequences, where N refers to all ambiguous base-codes as specified by IUPAC.
- Quality distribution
- Calculates the amount of bases that feature individual PHRED-scores in 64 bins from 0 to 63. This results in a three-dimensional table, where dimension 1 refers to the base-position, dimension 2 refers to the quality-score and dimension 3 to amounts of bases observed at that position with that quality score. PHRED-scores above 20 are considered good quality. It is normal to see the quality dropping off near the end of reads. Such low-quality ends can be trimmed off using the Trim Reads tool.