QC Report

	general
Report generated at	2019-11-16 00:04:03
Title	ENCSR936XTK (subsampled 1/50, chr19 and chrM Only)
Description	ZNF143 ChIP-seq on human GM12878
Pipeline version	v1.3.3
Pipeline type	tf
Genome	hg38_chr19_chrM
Paired-end per replicate	[True, True]
Aligner	bowtie2
Peak caller	spp
Control paired-end per replicate	[True, True]

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1	ctl2
Total Reads	1384648	1734696	1135028	1085984
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	150070	180208	106882	107693
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	10.8	10.4	9.4	9.9
Paired Reads	1384648	1734696	1135028	1085984
Paired Reads (QC-failed)	0	0	0	0
Read1	692324	867348	567514	542992
Read1 (QC-failed)	0	0	0	0
Read2	692324	867348	567514	542992
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	110910	128428	75034	75712
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	8.0	7.3999999999999995	6.6000000000000005	7.000000000000001
With itself	118268	138542	79904	80994
With itself (QC-failed)	0	0	0	0
Singletons	31802	41666	26978	26699
Singletons (QC-failed)	0	0	0	0
% Singleton	2.3	2.4	2.4	2.5
Diff. Chroms	0	0	2	6
Diff. Chroms (QC-failed)	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2
Unpaired Reads	0	0	0	0
Paired Reads	28515	27068	14825	15944
Unmapped Reads	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0
Paired Duplicate Reads	95	52	30	44
Paired Optical Duplicate Reads	0	1	0	0
% Duplicate Reads	0.3332	0.1921	0.20240000000000002	0.27599999999999997

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	56840	54032	29590	31800
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	56840	54032	29590	31800
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0
Paired Reads	56840	54032	29590	31800
Paired Reads (QC-failed)	0	0	0	0
Read1	28420	27016	14795	15900
Read1 (QC-failed)	0	0	0	0
Read2	28420	27016	14795	15900
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	56840	54032	29590	31800
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	100.0	100.0	100.0	100.0
With itself	56840	54032	29590	31800
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	24079	24161	8144	8473
Distinct Fragments	23992	24117	8133	8459
Positions with Two Read	87	42	11	12
NRF = Distinct/Total	0.996387	0.998179	0.998649	0.998348
PBC1 = OneRead/Distinct	0.996374	0.998217	0.998647	0.998463
PBC2 = OneRead/TwoRead	274.770115	573.190476	738.363636	703.833333

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	490	251
N1	336	189
N2	301	143
Np	511	245
N optimal	511	251
N conservative	490	251
Optimal Set	pooled-pr1_vs_pooled-pr2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.042857142857143	1.0244897959183674
Self Consistency Ratio	1.1162790697674418	1.3216783216783217
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	1472	1601

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	99.0	96.0	107.0	107.0
25 percentile	396.0	384.0	327.5	400.0
50 percentile (median)	396.0	384.0	400.0	400.0
75 percentile	396.0	384.0	400.0	400.0
Max size	457.0	417.0	758.0	758.0
Mean	388.5713315217391	379.30918176139915	362.9402390438247	381.79647749510764

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	27129	28285
Estimated Fragment Length	215	225
Cross-correlation at Estimated Fragment Length	0.166620142702605	0.0995979297625024
Phantom Peak	55	50
Cross-correlation at Phantom Peak	0.07393053	0.06487183
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.01531093	0.01813706
NSC (Normalized Strand Cross-correlation coeff.)	10.88243	5.491404
RSC (Relative Strand Cross-correlation coeff.)	2.581205	1.743046

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	0.027826119171271313	0.042776133405364576
Synthetic AUC	0.47970258979213914	0.47916570150109994
X-intercept	0.8491125145918764	0.816809841659433
Synthetic X-intercept	4.6382905671585126e-20	5.146075782684759e-19
Elbow Point	0.866698594191186	0.8367944765382581
Synthetic Elbow Point	0.5142923552146558	0.4827296689401493
JS Distance	0.330666797582514	0.31422570578123565
Synthetic JS Distance	0.5098388146136626	0.42480029203850417
% Genome Enriched	13.976872499426303	17.092599798457503
Diff. Enrichment	43.40936236301788	41.531295409999075
CHANCE Divergence	0.49954485530929726	0.4853099905037958

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	0.4070900774102745	0.3310630737340835	0.3794862772695285	0.2903464613562333	0.36963406052076003	0.2843129997038792	0.4070369435024172	0.37527960170286456	0.36826250090194096

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	0.28396709719315966	0.30830401125967627	0.21764880071068995	0.28670899776318637

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	0.24920629194025543	0.25900774102744545	0.16769692034350014	0.24770906991846453

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