| Reads (QC-passed) | Reads (QC-failed) | Dupes (QC-passed) | Dupes (QC-failed) | Mapped Reads | % Mapped |
---|---|---|---|---|---|---|
rep1 | 5193332 | 0 | 0 | 0 | 5049665 | 97.23 |
  | Unpaired Reads | Paired Reads | Unmapped Reads | Unpaired Dupes | Paired Dupes | Paired Opt. Dupes | % Dupes |
---|---|---|---|---|---|---|---|
rep1 | 4664401 | 0 | 0 | 28474 | 0 | 0 | 0.006105 |
  | Reads (QC-passed) | Reads (QC-failed) | Dupes (QC-passed) | Dupes (QC-failed) | Mapped Reads | % Mapped |
---|---|---|---|---|---|---|
rep1 | 4635927 | 0 | 0 | 0 | 4635927 | 100.00 |
  | Total Read Pairs | Distinct Read Pairs | One Read Pair | Two Read Pairs | NRF = Distinct/Total | PBC1 = OnePair/Distinct | PBC2 = OnePair/TwoPair |
---|---|---|---|---|---|---|---|
rep1 | 4659049 | 4631573 | 4607113 | 23352 | 0.994103 | 0.994719 | 197.289868 |
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 | 4631386 | 235 | 0.0722832373827486 | 75 | 0.07102321 | 1500 | 0.06507473 | 1.110773 | 1.211824 | 1 |
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