ENCSR936XTK (subsampled 1/66.67 reads)

ZNF143 ChIP-seq on human GM12878

Report generated at 2018-01-31 14:23:14

Pipeline type: TF ChIP-Seq

Peak caller: SPP

Flagstat QC (raw BAM)

rep1rep2ctl1ctl2
Total1037412129967811350281085984
Total(QC-failed)0000
Dupes0000
Dupes(QC-failed)0000
Mapped85367979778102181878
Mapped(QC-failed)0000
% Mapped8.23007.54007.14007.5400
Paired1037412129967811350281085984
Paired(QC-failed)0000
Read1518706649839567514542992
Read1(QC-failed)0000
Read2518706649839567514542992
Read2(QC-failed)0000
Properly Paired69328763475946060740
Properly Paired(QC-failed)0000
% Properly Paired6.68005.87005.24005.5900
With itself73921831416410265497
With itself(QC-failed)0000
Singletons11446148361691916381
Singletons(QC-failed)0000
% Singleton1.10001.14001.49001.5100
Diff. Chroms3107
Diff. Chroms (QC-failed)0000

Flagstat QC (filtered BAM)

rep1rep2ctl1ctl2
Total42702407123062832814
Total(QC-failed)0000
Dupes0000
Dupes(QC-failed)0000
Mapped42702407123062832814
Mapped(QC-failed)0000
% Mapped100.0000100.0000100.0000100.0000
Paired42702407123062832814
Paired(QC-failed)0000
Read121351203561531416407
Read1(QC-failed)0000
Read221351203561531416407
Read2(QC-failed)0000
Properly Paired42702407123062832814
Properly Paired(QC-failed)0000
% Properly Paired100.0000100.0000100.0000100.0000
With itself42702407123062832814
With itself(QC-failed)0000
Singletons0000
Singletons(QC-failed)0000
% Singleton0.00000.00000.00000.0000
Diff. Chroms0000
Diff. Chroms (QC-failed)0000

MarkDuplicate QC

rep1rep2ctl1ctl2
Unpaired Reads0000
Paired Reads21408203951534516451
Unmapped Reads0000
Unpaired Dupes0000
Paired Dupes57393144
Paired Opt. Dupes0000
% Dupes/1000.00270.00190.00200.0027

Library complexity QC

rep1rep2ctl1ctl2
Total Read Pairs181231830086749003
Distinct Read Pairs180721826586628989
One Read Pair180211823086508976
Two Read Pairs51351212
NRF = Distinct/Total0.99720.99810.99860.9984
PBC1 = OnePair/Distinct0.99720.99810.99860.9986
PBC2 = OnePair/TwoPair353.3529520.8571720.8333748.0000

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally


Enrichment (strand cross-correlation measures) QC

rep1rep2
Reads1968120319
Est. Fragment Len.210235
Corr. Est. Fragment Len.0.12180.0739
Phantom Peak5555
Corr. Phantom Peak0.05450.0443
Argmin. Corr.15001500
Min. Corr.0.01340.0139
NSC9.10665.3101
RSC2.63721.9700

NOTE1: For SE datasets, reads from replicates are randomly subsampled.
NOTE2: For PE datasets, the first end of each read-pair is selected and the reads are then randomly subsampled.


rep1
rep1
rep2
rep2

Fingerprint and JS distance

rep1rep2
% genome enriched0.02310.0348
AUC0.47660.4760
CHANCE divergence0.87990.8556
Elbow Point0.00000.0000
JS Distance0.89040.8677
Synthetic AUC0.51510.4984
Synthetic Elbow Point0.34310.3340
Synthetic JS Distance0.48950.4052
Synthetic X-intercept11.341413.7262
X-intercept45.501244.1376
diff. enrichment0.51860.5087

Enrichment QC (Fraction of reads in SPP raw peaks)

rep1rep2rep1-pr1rep2-pr1rep1-pr2rep2-pr2pooledppr1ppr2
Fraction of Reads in Peak0.45080.34660.40970.29900.41820.30720.40100.38770.3989


Reproducibility QC and Peak Detection Statistics

overlapIDR
Nt385269
N1288220
N224591
Np375263
N optimal385269
N conservative385269
Optimal Setrep1-rep2rep1-rep2
Conservative Setrep1-rep2rep1-rep2
Rescue Ratio1.02671.0228
Self Consistency Ratio1.17552.4176
reproducibilitypassborderline

Overlapping peaks


IDR (Irreproducible Discovery Rate) peaks


Enrichment QC (Fraction of reads in overlapping peaks)

rep1-rep2rep1-prrep2-prppr
Fraction of Reads in Peak0.29850.33800.22670.2966


Enrichment QC (Fraction of reads in IDR peaks)

rep1-rep2rep1-prrep2-prppr
Fraction of Reads in Peak0.27740.31090.15350.2744


IDR (Irreproducible Discovery Rate) plots

rep1-rep2
rep1-rep2
rep1-pr
rep1-pr
rep2-pr
rep2-pr
ppr
ppr