QC Report

	general
Report generated at	2019-07-13 15:41:09
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	bowtie2
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	30231793	23191870	23861084	27460091
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	24957432	18881467	19741671	22349006
Paired Reads	0	0	0	0
Unmapped Reads	0	0	0	0
Unpaired Dupes	1327012	765222	3282064	1023099
Paired Dupes	0	0	0	0
Paired Opt. Dupes	0	0	0	0
% Dupes/100	0.053171	0.040528	0.166251	0.045778

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	60127217	47393516	47463142	56139379
Mito. reads	155493	169103	172364	251409
Frac. of mito. reads	0.00258606680565	0.00356806192645	0.00363153370672	0.00447830033888
Total deduped reads	23630420	18116245	16459607	21325907
Mito. deduped reads	20709	20511	21060	21640
Frac. of deduped mito. reads	0.000876370373442	0.00113218826528	0.00127949591992	0.00101472823641
Total dup reads	1327012	765222	3282064	1023099
Mito. dup reads	87956	98142	102257	149356
Frac. of mito. dup reads	0.0662812393558	0.128252977567	0.0311563089568	0.14598391749

SAMstat (filtered/deduped BAM)

	rep1	rep2	ctl1	ctl2
Total	23630420	18116245	16459607	21325907
Total(QC-failed)	0	0	0	0
Dupes	0	0	0	0
Dupes(QC-failed)	0	0	0	0
Mapped	23630420	18116245	16459607	21325907
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)	24848767	18762814	19618354	22178010
Distinct Reads (Pairs)	23611510	18096891	16442560	21305404
One Read (Pair)	22496064	17516126	13673003	20484808
Two Reads (Pairs)	1030650	526060	2417214	789463
NRF = Distinct/Total	0.950209	0.964508	0.838121	0.960654
PBC1 = OnePair/Distinct	0.952758	0.967908	0.831562	0.961484
PBC2 = OnePair/TwoPair	21.827064	33.296822	5.656513	25.947775

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	127167	44561
N1	88910	29786
N2	95897	30585
Np	130524	48135
N optimal	130524	48135
N conservative	127167	44561
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.02639835806	1.08020466327
Self Consistency Ratio	1.07858508604	1.02682468274
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	299630	299540	48135	130524

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	66.0	64.0	65.0	65.0
25 percentile	264.0	256.0	260.0	260.0
50 percentile (median)	264.0	256.0	260.0	260.0
75 percentile	264.0	256.0	260.0	260.0
Max size	556.0	576.0	598.0	598.0
Mean	262.643506992	254.55856313	244.746899346	254.375938525

Alignment enrichment

Strand cross-correlation measures

	rep1	rep2
Reads	15000000	15000000
Est. Fragment Len.	105	90
Corr. Est. Fragment Len.	0.207615704208	0.217655054133
Phantom Peak	35	35
Corr. Phantom Peak	0.2347065	0.2464728
Argmin. Corr.	1500	1500
Min. Corr.	0.1787521	0.1788231
NSC	1.161473	1.217153
RSC	0.5158422	0.574015

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	0.246019036902	0.223251881873
AUC	0.487954196604	0.486233272512
CHANCE divergence	0.15497206972	0.200660170261
Elbow Point	3.38078255023e-58	2.36790118669e-44
JS Distance	0.597508067193	0.599807267071
Synthetic AUC	0.513812665717	0.521400386505
Synthetic Elbow Point	0.119739622596	0.14065935636
Synthetic JS Distance	0.297832520699	0.313898848423

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	0.176557264932	0.210798688796	0.185882657103	0.215267311069	0.185541880862	0.215737366608	0.186157850612	0.190252563178	0.190149612123

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	0.128890052606	0.101141686995	0.128416067566	0.13063836149

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	0.0818019805328	0.0623871677209	0.0768846955863	0.0848804035061

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