| Total Reads | % Aligned |
---|---|---|
rep1 | 32740762 | 97.94 |
  | Unpaired Reads | Paired Reads | Unmapped Reads | Unpaired Dupes | Paired Dupes | Paired Opt. Dupes | % Dupes |
---|---|---|---|---|---|---|---|
rep1 | 0 | 25421363 | 0 | 0 | 2909188 | 1651356 | 0.114439 |
  | Reads (QC-passed) | Reads (QC-failed) | Dupes (QC-passed) | Dupes (QC-failed) | Mapped Reads | % Mapped |
---|---|---|---|---|---|---|
rep1 | 45024350 | 0 | 0 | 0 | 45024350 | 100.00 |
  | Total Read Pairs | Distinct Read Pairs | One Read Pair | Two Read Pairs | NRF = Distinct/Total | PBC1 = OnePair/Distinct | PBC2 = OnePair/TwoPair |
---|---|---|---|---|---|---|---|
rep1 | 22424670 | 21793633 | 21188395 | 589450 | 0.971860 | 0.972229 | 35.946043 |
NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally
  | numReads | estFragLen | corr_estFragLen | PhantomPeak | corr_phantomPeak | argmin_corr | min_corr | phantomPeakCoef | relPhantomPeakCoef | QualityTag |
---|---|---|---|---|---|---|---|---|---|---|
rep1 | 21793633 | 0 | 0.238639063566729 | 55 | 0.2402565 | 1500 | 0.223495 | 1.06776 | 0.9035015 | 0 |
Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value
Important columns highlighted, but all/whole file can be stored for display