QC Report

	general
Report generated at	2019-07-13 14:57:21
Title	ENCSR000DYI
Description	CEBPB ChIP-seq on human A549 produced by the Snyder lab
Pipeline version	v1.2.2
Genome	hg38_google.tsv
Paired-end per replicate	[False, False]
Aligner	bwa
Peak caller	spp
Control paired-end per replicate	[False, False]

Alignment quality metrics

SAMstat (raw BAM)

	rep1	rep2	ctl1	ctl2
Total	30537463	23711730	24114469	28739630
Total(QC-failed)	0	0	0	0
Dupes	0	0	0	0
Dupes(QC-failed)	0	0	0	0
Mapped	30274746	23220534	23881180	27468951
Mapped(QC-failed)	0	0	0	0
% Mapped	0.0	0.0	0.0	0.0
Paired	0	0	0	0
Paired(QC-failed)	0	0	0	0
Read1	0	0	0	0
Read1(QC-failed)	0	0	0	0
Read2	0	0	0	0
Read2(QC-failed)	0	0	0	0
Properly Paired	0	0	0	0
Properly Paired(QC-failed)	0	0	0	0
% Properly Paired	0.0	0.0	0.0	0.0
With itself	0	0	0	0
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

Marking duplicates (filtered BAMs)

	rep1	rep2	ctl1	ctl2
Unpaired Reads	23054530	17329108	18232260	20521787
Paired Reads	0	0	0	0
Unmapped Reads	0	0	0	0
Unpaired Dupes	1182695	651709	3011607	880764
Paired Dupes	0	0	0	0
Paired Opt. Dupes	0	0	0	0
% Dupes/100	0.0513	0.037608	0.16518	0.042918

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	30274746	23220534	23881180	27468951
Mito. reads	130364	142226	146124	208227
Frac. of mito. reads	0.00430603117199	0.00612500987273	0.00611879312496	0.00758044965023
Total deduped reads	21871835	16677399	15220653	19641023
Mito. deduped reads	12877	12747	13139	13452
Frac. of deduped mito. reads	0.000588748040574	0.000764327818744	0.000863234974216	0.000684893042486
Total dup reads	1182695	651709	3011607	880764
Mito. dup reads	58138	60632	73979	99090
Frac. of mito. dup reads	0.0491572214307	0.0930353884939	0.0245646261282	0.112504598281

SAMstat (filtered/deduped BAM)

	rep1	rep2	ctl1	ctl2
Total	21871835	16677399	15220653	19641023
Total(QC-failed)	0	0	0	0
Dupes	0	0	0	0
Dupes(QC-failed)	0	0	0	0
Mapped	21871835	16677399	15220653	19641023
Mapped(QC-failed)	0	0	0	0
% Mapped	100.0	100.0	100.0	100.0
Paired	0	0	0	0
Paired(QC-failed)	0	0	0	0
Read1	0	0	0	0
Read1(QC-failed)	0	0	0	0
Read2	0	0	0	0
Read2(QC-failed)	0	0	0	0
Properly Paired	0	0	0	0
Properly Paired(QC-failed)	0	0	0	0
% Properly Paired	0.0	0.0	0.0	0.0
With itself	0	0	0	0
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)	22983515	17255729	18145142	20409245
Distinct Reads (Pairs)	21860128	16665253	15210785	19628350
One Read (Pair)	20831085	16136326	12643826	18877521
Two Reads (Pairs)	954716	482701	2241592	726308
NRF = Distinct/Total	0.951122	0.965781	0.838284	0.961738
PBC1 = OnePair/Distinct	0.952926	0.968262	0.831241	0.961748
PBC2 = OnePair/TwoPair	21.819143	33.429237	5.640556	25.991069

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	123178	43744
N1	85732	28780
N2	87652	28410
Np	126008	46864
N optimal	126008	46864
N conservative	123178	43744
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.02297488188	1.0713240673
Self Consistency Ratio	1.02239537162	1.01302358325
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	299841	299809	46864	126008

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	65.0	62.0	64.0	64.0
25 percentile	260.0	250.0	256.0	256.0
50 percentile (median)	260.0	250.0	256.0	256.0
75 percentile	260.0	250.0	256.0	256.0
Max size	555.0	569.0	595.0	595.0
Mean	258.760733189	248.7402613	241.669149027	250.671877976

Alignment enrichment

Strand cross-correlation measures

	rep1	rep2
Reads	15000000	15000000
Est. Fragment Len.	120	105
Corr. Est. Fragment Len.	0.209418557366	0.227804982176
Phantom Peak	40	40
Corr. Phantom Peak	0.1963714	0.2086889
Argmin. Corr.	1500	1500
Min. Corr.	0.1660973	0.1638962
NSC	1.260818	1.389935
RSC	1.430966	1.426767

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	0.23335886063	0.211460268789
AUC	0.487477646214	0.485650221759
CHANCE divergence	0.189811945443	0.238285076793
Elbow Point	8.79058149817e-54	9.33287340004e-41
JS Distance	0.619016582229	0.622789269334
Synthetic AUC	0.522936719531	0.496427849315
Synthetic Elbow Point	0.121506993215	0.141270711407
Synthetic JS Distance	0.300972473571	0.31480110074

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	0.183447216468	0.218936285018	0.194216485525	0.21567315057	0.194336527844	0.216308627387	0.193095948173	0.198105733082	0.198224309716

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	0.131802860635	0.103310139486	0.128625188213	0.13338503323

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	0.0848046691367	0.0642682967779	0.0778515506954	0.0876150755342

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