Runs

Help for per position statistics :

Quality : WARN = A warning will be issued if the lower quartile for any base is less than 10, or if the median for any base is less than 25. FAIL = This module will raise a failure if the lower quartile for any base is less than 5 or if the median for any base is less than 20.
GC% : WARN = This module issues a warning it the GC content of any base strays more than 5% from the mean GC content. FAIL = This module will fail if the GC content of any base strays more than 10% from the mean GC content.
N content : This module raises a warning if any position shows an N content of >5%. FAIL = This module will raise an error if any position shows an N content of >20%.
Per base content : WARN = This module issues a warning if the difference between A and T, or G and C is greater than 10% in any position. FAIL = This module will fail if the difference between A and T, or G and C is greater than 20% in any position.

Help for per sequence statistics :

Quality : WARN = A warning is raised if the most frequently observed mean quality is below 27 - this equates to a 0.2% error rate. FAIL = An error is raised if the most frequently observed mean quality is below 20 - this equates to a 1% error rate.
GC% : WARN = A warning is raised if the sum of the deviations from the normal distribution represents more than 15% of the reads. FAIL = This module will indicate a failure if the sum of the deviations from the normal distribution represents more than 30% of the reads.
Length distribution : WARN = This module will raise a warning if all sequences are not the same length. FAIL = This module will raise an error if any of the sequences have zero length.
Duplication level : WARN = This module will issue a warning if non-unique sequences make up more than 20% of the total. FAIL = This module will issue a error if non-unique sequences make up more than 50% of the total.
Kmer profiles : WARN = This module will issue a warning if any k-mer is enriched more than 3 fold overall, or more than 5 fold at any individual position. FAIL = This module will issue a error if any k-mer is enriched more than 10 fold at any individual base position.
Overrepresented sequences : WARN = This module will issue a warning if any sequence is found to represent more than 0.1% of the total. FAIL = This module will issue an error if any sequence is found to represent more than 1% of the total.

Analysis ReadsStats