Adapter Contamination

Adapter contamination is defined here as non-genetic sequences attached at either or both ends of the reads. The 'contamination' measure is the number of reads with a right or left match to the adapter sequence over the total number of reads. Mismatch rates are 10% on the left and 20% on the right with a minimum overlap of 10 nt.

  ShortRead:::.ppnCount(qa[["adapterContamination"]])