QC Report

	general
Report generated at	2019-07-14 12:31:43
Title	ENCSR936XTK
Description	ZNF143 ChIP-seq on human GM12878
Pipeline version	v1.2.2
Genome	hg38_google.tsv
Paired-end per replicate	[True, True]
Aligner	bowtie2
Peak caller	spp
Control paired-end per replicate	[True, True]

Alignment quality metrics

SAMstat (raw BAM)

	rep1	rep2	ctl1	ctl2
Total	69122852	86590386	90753054	86825372
Total(QC-failed)	0	0	0	0
Dupes	0	0	0	0
Dupes(QC-failed)	0	0	0	0
Mapped	68246710	83990125	89493723	85502393
Mapped(QC-failed)	0	0	0	0
% Mapped	0.0	0.0	0.0	0.0
Paired	69122852	86590386	90753054	86825372
Paired(QC-failed)	0	0	0	0
Read1	34561426	43295193	45376527	43412686
Read1(QC-failed)	0	0	0	0
Read2	34561426	43295193	45376527	43412686
Read2(QC-failed)	0	0	0	0
Properly Paired	67838132	83434596	88521292	84602752
Properly Paired(QC-failed)	0	0	0	0
% Properly Paired	0.0	0.0	0.0	0.0
With itself	67928558	83587578	88906784	84921146
With itself(QC-failed)	0	0	0	0
Singletons	318152	402547	586939	581247
Singletons(QC-failed)	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0
Diff. Chroms	32966	45352	143326	123769
Diff. Chroms (QC-failed)	0	0	0	0

Marking duplicates (filtered BAMs)

	rep1	rep2	ctl1	ctl2
Unpaired Reads	0	0	0	0
Paired Reads	30661438	37544768	39763292	37936610
Unmapped Reads	0	0	0	0
Unpaired Dupes	0	0	0	0
Paired Dupes	3708069	2863907	4071065	4068370
Paired Opt. Dupes	8611	24442	8563	8154
% Dupes/100	0.120936	0.07628	0.102382	0.107241

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8, for paired-end)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

Fraction of mitochondrial reads

	rep1	rep2	ctl1	ctl2
Total reads	98395238	124526452	130195163	125019035
Mito. reads	458726	292528	1093952	1236326
Frac. of mito. reads	0.0046620752114	0.00234912338143	0.00840240124743	0.00988910208753
Total deduped reads	53906738	69361722	71384454	67736480
Mito. deduped reads	254736	177030	540928	595586
Frac. of deduped mito. reads	0.00472549461257	0.0025522722749	0.00757767230383	0.00879269191431
Total dup reads	7416138	5727814	8142130	8136740
Mito. dup reads	45938	20900	102952	129894
Frac. of mito. dup reads	0.0061943291778	0.00364886150284	0.0126443571891	0.0159638872571

SAMstat (filtered/deduped BAM)

	rep1	rep2	ctl1	ctl2
Total	53906738	69361722	71384454	67736480
Total(QC-failed)	0	0	0	0
Dupes	0	0	0	0
Dupes(QC-failed)	0	0	0	0
Mapped	53906738	69361722	71384454	67736480
Mapped(QC-failed)	0	0	0	0
% Mapped	100.0	100.0	100.0	100.0
Paired	53906738	69361722	71384454	67736480
Paired(QC-failed)	0	0	0	0
Read1	26953369	34680861	35692227	33868240
Read1(QC-failed)	0	0	0	0
Read2	26953369	34680861	35692227	33868240
Read2(QC-failed)	0	0	0	0
Properly Paired	53906738	69361722	71384454	67736480
Properly Paired(QC-failed)	0	0	0	0
% Properly Paired	100.0	100.0	100.0	100.0
With itself	53906738	69361722	71384454	67736480
With itself(QC-failed)	0	0	0	0
Singletons	0	0	0	0
Singletons(QC-failed)	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0
Diff. Chroms (QC-failed)	0	0	0	0

Filtered and duplicates removed

Library complexity quality metrics

Library complexity (filtered non-mito BAM)

	rep1	rep2	ctl1	ctl2
Total Reads (Pairs)	30511101	37445803	39441352	37573870
Distinct Reads (Pairs)	26826006	34592364	35421785	33570487
One Read (Pair)	23539787	31940816	32026832	29992121
Two Reads (Pairs)	2928828	2463967	2981438	3206670
NRF = Distinct/Total	0.879221	0.923798	0.898087	0.893453
PBC1 = OnePair/Distinct	0.877499	0.923349	0.904156	0.893407
PBC2 = OnePair/TwoPair	8.037272	12.963167	10.742075	9.353043

Mitochondrial reads are filtered out by default. The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads in a dataset; it is the ratio between the number of positions in the genome that uniquely mapped reads map to and the total number of uniquely mappable reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with AT LEAST one read pair. PBC1 is the primary measure, and the PBC1 should be close to 1. Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking, 0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with EXACTLY two read pairs. The PBC2 should be significantly greater than 1.

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

Replication quality metrics

IDR (Irreproducible Discovery Rate) plots

Reproducibility QC and peak detection statistics

	overlap	idr
Nt	95107	27729
N1	84148	21472
N2	68098	14412
Np	98784	29925
N optimal	98784	29925
N conservative	95107	27729
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.03866171785	1.07919506654
Self Consistency Ratio	1.23568974126	1.48986955315
Reproducibility Test	pass	pass

Reproducibility QC

N1: Replicate 1 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Ni: Replicate i self-consistent peaks (comparing two pseudoreplicates generated by subsampling RepX reads)
Nt: True Replicate consistent peaks (comparing true replicates Rep1 vs Rep2)
Np: Pooled-pseudoreplicate consistent 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'

Number of peaks called

	rep1	rep2	idr_opt	overlap_opt
Number of peaks	299584	299394	29925	98784

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	110.0	102.0	111.0	111.0
25 percentile	440.0	410.0	444.0	444.0
50 percentile (median)	440.0	410.0	444.0	444.0
75 percentile	440.0	410.0	444.0	444.0
Max size	1421.0	1375.0	1421.0	1421.0
Mean	438.658820231	409.342258028	420.570359231	436.627065112

Alignment enrichment

Strand cross-correlation measures

	rep1	rep2
Reads	15000000	15000000
Est. Fragment Len.	220	215
Corr. Est. Fragment Len.	0.253219558374	0.238839459296
Phantom Peak	50	50
Corr. Phantom Peak	0.241782	0.2503202
Argmin. Corr.	1500	1500
Min. Corr.	0.1681672	0.1863845
NSC	1.505761	1.281434
RSC	1.15537	0.8204334

Performed on subsampled reads

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.

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

Fingerprint and Jensen-Shannon distance

	rep1	rep2
% genome enriched	0.254362621275	0.283591256637
AUC	0.495220449248	0.495789120855
CHANCE divergence	0.108236653598	0.0994680032228
Elbow Point	0.0	0.0
JS Distance	0.654533968024	0.61479714749
Synthetic AUC	0.49898592288	0.505143324061
Synthetic Elbow Point	0.214235667237	0.169080912161
Synthetic JS Distance	0.349051726465	0.302123805992

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for spp raw peaks

	rep1	rep2	rep1-pr1	rep2-pr1	rep1-pr2	rep2-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.246909928916	0.182553504755	0.263605437739	0.194988770059	0.263475546112	0.196081526243	0.201589030066	0.211218396822	0.211206029547

FRiP for overlap peaks

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.133030607287	0.161059283491	0.09770875326	0.135237594395

FRiP for IDR peaks

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.0946362493279	0.1143823114	0.0627337186093	0.09670376671

For raw peaks (e.g. spp and macs2):

repX: Peak from true replicate X
repX-prY: Peak from Yth pseudoreplicates from replicate X
pooled: Peak from pooled true replicates (pool of rep1, rep2, ...)
pooled-pr1: Peak from 1st pooled pseudo replicate (pool of rep1-pr1, rep2-pr1, ...)
pooled-pr2: Peak from 2nd pooled pseudo replicate (pool of rep1-pr2, rep2-pr2, ...)

For overlap/IDR peaks:

repX_vs_repY: Comparing two peaks from true replicates X and Y
repX-pr1_vs_repX-pr2: Comparing two peaks from both pseudoreplicates from replicate X
pooled-pr1_vs_pooled-pr2: Comparing two peaks from 1st and 2nd pooled pseudo replicates