QC Report

	general
Report generated at	2019-11-20 15:05:39
Title	ENCSR936XTK
Description	ZNF143 ChIP-seq on human GM12878
Pipeline version	v1.3.4
Pipeline type	tf
Genome	hg38
Aligner	bowtie2
Sequencing endedness	{'rep1': {'paired_end': True}, 'rep2': {'paired_end': True}, 'ctl1': {'paired_end': True}, 'ctl2': {'paired_end': True}}
Peak caller	spp

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1	ctl2
Total Reads	69122852	86590386	90753054	86825372
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	68199569	83912929	89404845	85411524
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	98.7	96.89999999999999	98.5	98.4
Paired Reads	69122852	86590386	90753054	86825372
Paired Reads (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 Reads	67803592	83381260	88446836	84530314
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	98.1	96.3	97.5	97.39999999999999
With itself	67888798	83525240	88825402	84840910
With itself (QC-failed)	0	0	0	0
Singletons	310771	387689	579443	570614
Singletons (QC-failed)	0	0	0	0
% Singleton	0.4	0.4	0.6	0.7000000000000001
Diff. Chroms	22493	29958	109194	94732
Diff. Chroms (QC-failed)	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2
Unpaired Reads	0	0	0	0
Paired Reads	30430331	37273155	39292512	37521960
Unmapped Reads	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0
Paired Duplicate Reads	3675532	2841181	3981072	3998345
Paired Optical Duplicate Reads	8548	24155	8406	8056
% Duplicate Reads	12.0785	7.6226	10.1319	10.656

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)

SAMstat (filtered/deduped BAM)

	rep1	rep2	ctl1	ctl2
Total Reads	53509598	68863948	70622880	67047230
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	53509598	68863948	70622880	67047230
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0
Paired Reads	53509598	68863948	70622880	67047230
Paired Reads (QC-failed)	0	0	0	0
Read1	26754799	34431974	35311440	33523615
Read1 (QC-failed)	0	0	0	0
Read2	26754799	34431974	35311440	33523615
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	53509598	68863948	70622880	67047230
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	100.0	100.0	100.0	100.0
With itself	53509598	68863948	70622880	67047230
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

Sequence quality metrics (filtered/deduped BAM)

Open chromatin assays are known to have significant GC bias. Please take this into consideration as necessary.

Library complexity quality metrics

Library complexity (filtered non-mito BAM)

	rep1	rep2	ctl1	ctl2
Total Fragments	30280428	37174715	38972024	37160721
Distinct Fragments	26627720	34343890	35041982	33226886
Positions with Two Read	2904534	2444971	2939500	3166313
NRF = Distinct/Total	0.879371	0.923851	0.899157	0.89414
PBC1 = OneRead/Distinct	0.87764	0.923398	0.90476	0.89385
PBC2 = OneRead/TwoRead	8.045884	12.970733	10.785707	9.379948

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. See more details at the ENCODE portal standard for ChIP-Seq pipeline

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	94929	27499
N1	83933	21946
N2	67259	14072
Np	98532	29761
N optimal	98532	29761
N conservative	94929	27499
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.037954681920172	1.0822575366376959
Self Consistency Ratio	1.2479073432551777	1.55955088118249
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 raw peaks

	rep1	rep2
Number of peaks	299605	299465

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	111.0	100.0	111.0	111.0
25 percentile	444.0	400.0	444.0	444.0
50 percentile (median)	444.0	400.0	444.0	444.0
75 percentile	444.0	400.0	444.0	444.0
Max size	1422.0	1369.0	1422.0	1422.0
Mean	442.57590160377833	399.43178668625717	420.402170625987	436.62252872163356

Enrichment / Signal-to-noise ratio

Strand cross-correlation measures (trimmed/filtered SE BAM)

	rep1	rep2
Number of Subsampled Reads	15000000	15000000
Estimated Fragment Length	225	210
Cross-correlation at Estimated Fragment Length	0.248728899064887	0.229513459729301
Phantom Peak	55	55
Cross-correlation at Phantom Peak	0.1872022	0.1929582
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.1387036	0.1622947
NSC (Normalized Strand Cross-correlation coeff.)	1.793241	1.414177
RSC (Relative Strand Cross-correlation coeff.)	2.268628	2.192146

Performed on subsampled (15000000) reads mapped from FASTQs that are trimmed to 50. Such FASTQ trimming and subsampling reads are for cross-corrleation analysis only. Untrimmed FASTQs are used for all the other analyses.

NOTE1: For SE datasets, reads from replicates are randomly subsampled to 15000000.
NOTE2: For PE datasets, the first end (R1) of each read-pair is selected and trimmed to 50 the reads are then randomly subsampled to 15000000.

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

Jensen-Shannon distance (filtered/deduped BAM)

	rep1	rep2
AUC	0.2536078629793387	0.2832876244897156
Synthetic AUC	0.495214842660931	0.49578043779370823
X-intercept	0.10873902873023172	0.0996921046844073
Synthetic X-intercept	0.0	0.0
Elbow Point	0.6563588379950817	0.6155387168362757
Synthetic Elbow Point	0.4998866984172783	0.5004638855712935
JS Distance	0.21810209741121928	0.17190962171426702
Synthetic JS Distance	0.35029970710339703	0.30244217373989163
% Genome Enriched	28.817002219245456	32.58951956334846
Diff. Enrichment	24.597780584105593	20.559528093285994
CHANCE Divergence	0.21000109692756722	0.17528583040824947

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	0.24592161951954863	0.1807447200093727	0.2631918384738439	0.19493401685305642	0.2630116661691858	0.1943553976893686	0.2007630962986069	0.2097771652416256	0.20987810894812362

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	0.132298936569183	0.159811049225225	0.0964785957377872	0.13441311082053634

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	0.09386920110985425	0.11405520183500538	0.06198790693789441	0.09597179606121735

For spp raw peaks:

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