number of reads passing filter Run QC Raw data are filtered to remove any reads that do not meet the overall quality as measured by a chastity filter. The chastity of a base call is calculated as the ratio of the brightest intensity divided by the sum of the brightest and second brightest intensities. Clusters passing filter are represented by PF in analysis reports. Clusters pass filter if no more than one base call in the first 25 cycles has a chastity of < 0.6. 0.92 URI: http://support.illumina.com/sequencing/sequencing_instruments/miseq/questions.html Output from MiSeq Number of Reads Passing Filter assembly quality control datum