QC Report

	general
Report generated at	2019-07-23 08:19:39
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	29153381	35494991	37930076	36107762
Unmapped Reads	0	0	0	0
Unpaired Dupes	0	0	0	0
Paired Dupes	3532920	2709855	3894103	3874385
Paired Opt. Dupes	8562	24275	8525	8111
% Dupes/100	0.121184	0.076345	0.102665	0.107301

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	51240922	65570272	68071946	64466754
Mito. deduped reads	98620	73860	214618	230650
Frac. of deduped mito. reads	0.00192463359656	0.00112642509703	0.00315281129175	0.00357781314691
Total dup reads	7065840	5419710	7788206	7748770
Mito. dup reads	20240	10468	45304	55862
Frac. of mito. dup reads	0.00286448603422	0.00193146865792	0.00581700073162	0.00720914416094

SAMstat (filtered/deduped BAM)

	rep1	rep2	ctl1	ctl2
Total	51240922	65570272	68071946	64466754
Total(QC-failed)	0	0	0	0
Dupes	0	0	0	0
Dupes(QC-failed)	0	0	0	0
Mapped	51240922	65570272	68071946	64466754
Mapped(QC-failed)	0	0	0	0
% Mapped	100.0	100.0	100.0	100.0
Paired	51240922	65570272	68071946	64466754
Paired(QC-failed)	0	0	0	0
Read1	25620461	32785136	34035973	32233377
Read1(QC-failed)	0	0	0	0
Read2	25620461	32785136	34035973	32233377
Read2(QC-failed)	0	0	0	0
Properly Paired	51240922	65570272	68071946	64466754
Properly Paired(QC-failed)	0	0	0	0
% Properly Paired	100.0	100.0	100.0	100.0
With itself	51240922	65570272	68071946	64466754
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)	29093951	35452827	37800115	35964506
Distinct Reads (Pairs)	25571156	32748222	33928682	32118090
One Read (Pair)	22431335	30235703	30661181	28681729
Two Reads (Pairs)	2796921	2334103	2868289	3078099
NRF = Distinct/Total	0.878917	0.923713	0.897581	0.89305
PBC1 = OnePair/Distinct	0.877212	0.923278	0.903695	0.893009
PBC2 = OnePair/TwoPair	8.02001	12.953885	10.689711	9.318001

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

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	0.24011929833	0.267542440612
AUC	0.495097837353	0.495669896341
CHANCE divergence	0.150964143267	0.142029449104
Elbow Point	0.0	0.0
JS Distance	0.645741075802	0.603314773534
Synthetic AUC	0.500583887458	0.505881863464
Synthetic Elbow Point	0.219114697914	0.172191362831
Synthetic JS Distance	0.352356534204	0.306843306467