QC Report

	general
Report generated at	2019-07-14 09:36:00
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	bwa
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	68063712	83658387	89164565	85203319
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	67691510	83126958	88383742	84455733
Properly Paired(QC-failed)	0	0	0	0
% Properly Paired	0.0	0.0	0.0	0.0
With itself	67846541	83375973	88810063	84838815
With itself(QC-failed)	0	0	0	0
Singletons	217171	282414	354502	364504
Singletons(QC-failed)	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0
Diff. Chroms	28970	44892	123377	113675
Diff. Chroms (QC-failed)	0	0	0	0

Marking duplicates (filtered BAMs)

	rep1	rep2	ctl1	ctl2
Unpaired Reads	0	0	0	0
Paired Reads	30291259	37072602	39854681	38118550
Unmapped Reads	0	0	0	0
Unpaired Dupes	0	0	0	0
Paired Dupes	3664057	2833119	4092825	4128511
Paired Opt. Dupes	8743	24855	8937	8553
% Dupes/100	0.120961	0.076421	0.102694	0.108307

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	68063712	83658387	89164565	85203319
Mito. reads	451940	287842	1075934	1215613
Frac. of mito. reads	0.00663995522313	0.00344068312003	0.0120668339491	0.0142672024314
Total deduped reads	53254404	68478966	71523712	67980078
Mito. deduped reads	321986	217706	744388	819732
Frac. of deduped mito. reads	0.00604618540093	0.00317916599383	0.0104075694505	0.0120584151139
Total dup reads	7328114	5666238	8185650	8257022
Mito. dup reads	62316	26296	163534	208426
Frac. of mito. dup reads	0.00850368867078	0.00464082165274	0.0199781324635	0.0252422725772

SAMstat (filtered/deduped BAM)

	rep1	rep2	ctl1	ctl2
Total	53254404	68478966	71523712	67980078
Total(QC-failed)	0	0	0	0
Dupes	0	0	0	0
Dupes(QC-failed)	0	0	0	0
Mapped	53254404	68478966	71523712	67980078
Mapped(QC-failed)	0	0	0	0
% Mapped	100.0	100.0	100.0	100.0
Paired	53254404	68478966	71523712	67980078
Paired(QC-failed)	0	0	0	0
Read1	26627202	34239483	35761856	33990039
Read1(QC-failed)	0	0	0	0
Read2	26627202	34239483	35761856	33990039
Read2(QC-failed)	0	0	0	0
Properly Paired	53254404	68478966	71523712	67980078
Properly Paired(QC-failed)	0	0	0	0
% Properly Paired	100.0	100.0	100.0	100.0
With itself	53254404	68478966	71523712	67980078
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)	30099108	36950601	39400720	37604471
Distinct Reads (Pairs)	26466206	34130627	35389661	33580171
One Read (Pair)	23226034	31510426	31987615	29976868
Two Reads (Pairs)	2888067	2434584	2993615	3230526
NRF = Distinct/Total	0.879302	0.923683	0.898198	0.892983
PBC1 = OnePair/Distinct	0.877573	0.92323	0.903869	0.892696
PBC2 = OnePair/TwoPair	8.042069	12.942838	10.68528	9.279253

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	94395	27396
N1	83224	20742
N2	66271	14179
Np	97905	28472
N optimal	97905	28472
N conservative	94395	27396
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.03718417289	1.03927580669
Self Consistency Ratio	1.25581325165	1.46286762113
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	299503	299314	28472	97905

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	110.0	99.0	110.0	110.0
25 percentile	440.0	396.0	440.0	440.0
50 percentile (median)	440.0	396.0	440.0	440.0
75 percentile	440.0	396.0	440.0	440.0
Max size	1900.0	1366.0	1924.0	1924.0
Mean	438.660928271	395.465992236	416.475414442	432.891364077

Alignment enrichment

Strand cross-correlation measures

	rep1	rep2
Reads	15000000	15000000
Est. Fragment Len.	225	210
Corr. Est. Fragment Len.	0.254989531232	0.238009871544
Phantom Peak	50	50
Corr. Phantom Peak	0.2034027	0.2127357
Argmin. Corr.	1500	1500
Min. Corr.	0.1469003	0.1698985
NSC	1.735799	1.400895
RSC	1.913004	1.590003

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	0.253084641843	0.28284376826
AUC	0.495213192319	0.495774226111
CHANCE divergence	0.109013409253	0.100348476639
Elbow Point	0.0	0.0
JS Distance	0.658133020911	0.616301829152
Synthetic AUC	0.507394657423	0.504944745786
Synthetic Elbow Point	0.218110008382	0.171867245381
Synthetic JS Distance	0.351742592038	0.303263760136

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	0.245311389327	0.179917818687	0.26278401781	0.194169167109	0.262019099978	0.194301511575	0.20014044792	0.20947232562	0.2095674035

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	0.131240096534	0.158366013055	0.0952495749419	0.133278536196

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	0.0928734665516	0.111554303074	0.0615353862498	0.0940136745417

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