Flagstat (raw) QC
| Total | 12945296 |
|---|---|
| Total(QC-failed) | 0 |
| Dupes | 0 |
| Dupes(QC-failed) | 0 |
| Mapped | 10995413 |
| Mapped(QC-failed) | 0 |
| % Mapped | 84.94 |
| Paired | 12945296 |
| Paired(QC-failed) | 0 |
| Read1 | 6472648 |
| Read1(QC-failed) | 0 |
| Read2 | 6472648 |
| Read2(QC-failed) | 0 |
| Properly Paired | 10910832 |
| Properly Paired(QC-failed) | 0 |
| % Properly Paired | 84.28 |
| With itself | 10979372 |
| With itself(QC-failed) | 0 |
| Singletons | 16041 |
| Singletons(QC-failed) | 0 |
| % Singleton | 0.12 |
| Diff. Chroms | 1732 |
| Diff. Chroms (QC-failed) | 0 |
Dup. QC
| Unpaired Reads | 0 |
|---|---|
| Paired Reads | 3181122 |
| Unmapped Reads | 0 |
| Unpaired Dupes | 0 |
| Paired Dupes | 326296 |
| Paired Opt. Dupes | 54519 |
| % Dupes/100 | 0.102573 |
Flagstat (filtered) QC
| Total | 5709652 |
|---|---|
| Total(QC-failed) | 0 |
| Dupes | 0 |
| Dupes(QC-failed) | 0 |
| Mapped | 5709652 |
| Mapped(QC-failed) | 0 |
| % Mapped | 100.00 |
| Paired | 5709652 |
| Paired(QC-failed) | 0 |
| Read1 | 2854826 |
| Read1(QC-failed) | 0 |
| Read2 | 2854826 |
| Read2(QC-failed) | 0 |
| Properly Paired | 5709652 |
| Properly Paired(QC-failed) | 0 |
| % Properly Paired | 100.00 |
| With itself | 5709652 |
| With itself(QC-failed) | 0 |
| Singletons | 0 |
| Singletons(QC-failed) | 0 |
| % Singleton | 0.00 |
| Diff. Chroms | 0 |
| Diff. Chroms (QC-failed) | 0 |
Library Complexity QC
| Total Read Pairs | 3120076 |
|---|---|
| Distinct Read Pairs | 2808673 |
| One Read Pair | 2595543 |
| Two Read Pairs | 170627 |
| NRF = Distinct/Total | 0.900194 |
| PBC1 = OnePair/Distinct | 0.924117 |
| PBC2 = OnePair/TwoPair | 15.211795 |
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
Enrichment QC (strand cross-correlation measures)
| Reads | 2804808 |
|---|---|
| Est. Fragment Len. | 0 |
| Corr. Est. Fragment Len. | 0.881194557737618 |
| Phantom Peak | 40 |
| Corr. Phantom Peak | 0.8050642 |
| Argmin. Corr. | 1500 |
| Min. Corr. | 0.7067081 |
| NSC | 1.2469 |
| RSC | 1.774028 |
NOTE: One end of each read-pair is randomly selected and the reads are then randomly subsampled to a max of 25M
- 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
Number of peaks
| rep1 | 4659 |
|---|---|
| rep1-pr1 | 4241 |
| rep1-pr2 | 4268 |
- ppr1: Raw peaks called on the first pooled pseudoreplicates
- ppr2: Raw peaks called on the second pooled pseudoreplicates
- repi: Raw peaks called on true replicate i
- repi-pr1 : Raw peaks called on the first pseudoreplicate from replicate i
- repi-pr2 : Raw peaks called on the second pseudoreplicates from replicate i
- overlap : Overlapped peaks (filtered if blacklist exists)
Enrichment QC (Fraction of reads in overlapping peaks)
| Fraction of Reads in Peak | 0.53102 |
|---|
- ppr: Overlapping peaks comparing pooled pseudo replicates
- rep1-pr: Overlapping peaks comparing pseudoreplicates from replicate 1
- rep2-pr: Overlapping peaks comparing pseudoreplicates from replicate 2
- repi-repj: Overlapping peaks comparing true replicates (rep i vs. rep j)
Reproducibility QC and Peak Detection Statistics (Overlapping peaks)
| Nt | 0 |
|---|---|
| N1 | 4046 |
| N2 | 0 |
| Np | 0 |
| N optimal | 4046 |
| N conservative | 4046 |
| Optimal Set | self_pseudo_rep_rep1 |
| Conservative Set | self_pseudo_rep_rep1 |
| Rescue Ratio | 0.0 |
| Self Consistency Ratio | 1.0 |
| Reproducibility Test | pass |
- N1: Replicate 1 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
- N2: Replicate 2 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
- Nt: True Replicate consisten overlapping peaks (comparing true replicates Rep1 vs Rep2 )
- Np: Pooled-pseudoreplicate consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2 )
- Self-consistency Ratio: max(N1,N2) / min (N1,N2)
- Rescue Ratio: max(Np,Nt) / min (Np,Nt)
- Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'