QC Report

	general
Report generated at	2021-09-01 03:36:18
Title	unc-3_RW12259_lateembryonic_1_2
Description	gevirl
Pipeline version	v1.3.6
Pipeline type	tf
Genome	WS245chr
Aligner	bwa
Sequencing endedness	{'rep1': {'paired_end': True}, 'rep2': {'paired_end': True}, 'ctl1': {'paired_end': True}}
Peak caller	spp

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1
Total Reads	12120978	10737376	13640338
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	12088428	10707319	13619798
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.7	99.7	99.8
Paired Reads	12120978	10737376	13640338
Paired Reads (QC-failed)	0	0	0
Read1	6060489	5368688	6820169
Read1 (QC-failed)	0	0	0
Read2	6060489	5368688	6820169
Read2 (QC-failed)	0	0	0
Properly Paired Reads	11986304	10571256	13473136
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.9	98.5	98.8
With itself	12074530	10694444	13607132
With itself (QC-failed)	0	0	0
Singletons	13898	12875	12666
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	4475	4186	20302
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	5372516	4721219	6169202
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	779217	694493	1000239
Paired Optical Duplicate Reads	77731	65518	111220
% Duplicate Reads	14.5038	14.71	16.2134

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
Total Reads	9186598	8053452	10337926
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	9186598	8053452	10337926
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	9186598	8053452	10337926
Paired Reads (QC-failed)	0	0	0
Read1	4593299	4026726	5168963
Read1 (QC-failed)	0	0	0
Read2	4593299	4026726	5168963
Read2 (QC-failed)	0	0	0
Properly Paired Reads	9186598	8053452	10337926
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	9186598	8053452	10337926
With itself (QC-failed)	0	0	0
Singletons	0	0	0
Singletons (QC-failed)	0	0	0
% Singleton	0.0	0.0	0.0
Diff. Chroms	0	0	0
Diff. Chroms (QC-failed)	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
Total Fragments	5348022	4696152	6138787
Distinct Fragments	4578669	4011592	5148760
Positions with Two Read	598072	529343	747972
NRF = Distinct/Total	0.856143	0.85423	0.838726
PBC1 = OneRead/Distinct	0.851968	0.850017	0.832773
PBC2 = OneRead/TwoRead	6.522424	6.441799	5.732499

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	20727	631
N1	26719	353
N2	26437	384
Np	18706	622
N optimal	20727	631
N conservative	20727	631
Optimal Set	rep1_vs_rep2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.1080402010050252	1.0144694533762058
Self Consistency Ratio	1.0106668684041307	1.0878186968838528
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	51663	55070

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	65.0	60.0	66.0	66.0
25 percentile	260.0	240.0	264.0	264.0
50 percentile (median)	260.0	240.0	264.0	264.0
75 percentile	260.0	240.0	264.0	264.0
Max size	260.0	240.0	264.0	264.0
Mean	259.9345566459555	239.95667332485928	251.83201267828844	263.6295653012978

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	5038082	4442437
Estimated Fragment Length	170	155
Cross-correlation at Estimated Fragment Length	0.601681027863744	0.570521901687862
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6023154	0.5712544
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.5979297	0.5668295
NSC (Normalized Strand Cross-correlation coeff.)	1.006274	1.006514
RSC (Relative Strand Cross-correlation coeff.)	0.8553544	0.8344689

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	0.4094902213909369	0.4055673931230841
Synthetic AUC	0.4978808339670032	0.49773104005924007
X-intercept	0.019830214885532743	0.02002378747725023
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5108580254797407	0.5148013186883361
Synthetic Elbow Point	0.5016084685957305	0.5030842494080251
JS Distance	0.030620409982029556	0.035918973175137016
Synthetic JS Distance	0.13291063219626714	0.13840658615567827
% Genome Enriched	43.56261374884256	43.61250359206871
Diff. Enrichment	9.16609852906714	9.697949441223736
CHANCE Divergence	0.07792451137483057	0.08246794350051671

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	0.252296551998901	0.2625199728017253	0.3765025145320358	0.3972520106905709	0.39158465224768785	0.3936433718112432	0.5512750833089232	0.23533223681691912	0.250474476637188

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	0.10524998477382606	0.137772764194101	0.13554460869699106	0.09665441805563209

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	0.007062856546239715	0.004757582730843344	0.007427870682037963	0.0073423800975055175

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