| Unpaired Reads | Paired Reads | Unmapped Reads | Unpaired Dupes | Paired Dupes | Paired Opt. Dupes | % Dupes |
---|---|---|---|---|---|---|---|
rep1 | 20991724 | 0 | 0 | 2606962 | 0 | 0 | 0.12419 |
  | Reads (QC-passed) | Reads (QC-failed) | Dupes (QC-passed) | Dupes (QC-failed) | Mapped Reads | % Mapped |
---|---|---|---|---|---|---|
rep1 | 18384762 | 0 | 0 | 0 | 18384762 | 100.00 |
  | Total Read Pairs | Distinct Read Pairs | One Read Pair | Two Read Pairs | NRF = Distinct/Total | PBC1 = OnePair/Distinct | PBC2 = OnePair/TwoPair |
---|---|---|---|---|---|---|---|
rep1 | 20979278 | 18684813 | 16694071 | 1750423 | 0.890632 | 0.893457 | 9.537164 |
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 | NSC | RSC |
---|---|---|---|---|---|---|---|---|---|
rep1 | 15000000 | 145 | 0.266724316314493 | 55 | 0.2289182 | 1500 | 0.1735547 | 1.536832 | 1.682869 |
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
Nt | N1 | N2 | Np | conservative_set | optimal_set | rescue_ratio | self_consistency_ratio | reproducibility |
---|---|---|---|---|---|---|---|---|
0 | 35343 | 0 | 0 | N/A | N/A | NaN | 1.0 | 1 |