Bowtie2 QC (all)
| Total Reads | % Aligned | |
|---|---|---|
| rep1 | 18199334 | 97.31 |
Dup QC (all)
| Unpaired Reads | Paired Reads | Unmapped Reads | Unpaired Dupes | Paired Dupes | Paired Opt. Dupes | % Dupes | |
|---|---|---|---|---|---|---|---|
| rep1 | 0 | 15379664 | 0 | 0 | 2212163 | 1426690 | 0.143837 |
Flagstat QC (all, filtered)
| Reads (QC-passed) | Reads (QC-failed) | Dupes (QC-passed) | Dupes (QC-failed) | Mapped Reads | % Mapped | |
|---|---|---|---|---|---|---|
| rep1 | 26335002 | 0 | 0 | 0 | 26335002 | 100.00 |
PBC QC (all)
| Total Read Pairs | Distinct Read Pairs | One Read Pair | Two Read Pairs | NRF = Distinct/Total | PBC1 = OnePair/Distinct | PBC2 = OnePair/TwoPair | |
|---|---|---|---|---|---|---|---|
| rep1 | 13087391 | 12648913 | 12374489 | 237731 | 0.966496 | 0.978305 | 52.052484 |
NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally
- 0-0.5 is severe bottlenecking
- 0.5-0.8 is moderate bottlenecking
- 0.8-0.9 is mild bottlenecking
- 0.9-1.0 is no bottlenecking
Cross-correlation QC (all)
rep1
| numReads | estFragLen | corr_estFragLen | PhantomPeak | corr_phantomPeak | argmin_corr | min_corr | phantomPeakCoef | relPhantomPeakCoef | QualityTag | |
|---|---|---|---|---|---|---|---|---|---|---|
| rep1 | 12648909 | 0 | 0.274860018582327 | 95 | 0.2719482 | 1500 | 0.1168226 | 2.352799 | 1.018771 | 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
IDR QC (idr)
151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_IDR_final.qc
| Nt | N1 | Np | conservative_set | optimal_set | rescue_ratio | self_consistency_ratio | reproducibility |
|---|---|---|---|---|---|---|---|
| 0 | 90385 | 0 | N/A | N/A | NaN | 1.0 | 1 |
