QC Report

	general
Report generated at	2021-08-28 17:27:53
Title	D2030.7_RW12302_youngadult_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	18028236	16431096	17930600
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	17997123	16393286	17895186
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.8	99.8	99.8
Paired Reads	18028236	16431096	17930600
Paired Reads (QC-failed)	0	0	0
Read1	9014118	8215548	8965300
Read1 (QC-failed)	0	0	0
Read2	9014118	8215548	8965300
Read2 (QC-failed)	0	0	0
Properly Paired Reads	17921288	16338998	17818884
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.4	99.4	99.4
With itself	17985042	16382934	17881358
With itself (QC-failed)	0	0	0
Singletons	12081	10352	13828
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	8284	5236	15144
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	8092235	7453545	8187868
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1408468	1104776	1115625
Paired Optical Duplicate Reads	141834	107158	128158
% Duplicate Reads	17.4052	14.822199999999999	13.625300000000001

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	13367534	12697538	14144486
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	13367534	12697538	14144486
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	13367534	12697538	14144486
Paired Reads (QC-failed)	0	0	0
Read1	6683767	6348769	7072243
Read1 (QC-failed)	0	0	0
Read2	6683767	6348769	7072243
Read2 (QC-failed)	0	0	0
Properly Paired Reads	13367534	12697538	14144486
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	13367534	12697538	14144486
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	8061068	7411592	8113591
Distinct Fragments	6662773	6318309	7014079
Positions with Two Read	1021586	852810	883332
NRF = Distinct/Total	0.826537	0.85249	0.864485
PBC1 = OneRead/Distinct	0.820509	0.847076	0.859421
PBC2 = OneRead/TwoRead	5.35135	6.27583	6.824216

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	44845	2777
N1	24839	2464
N2	26352	1811
Np	35947	3082
N optimal	44845	3082
N conservative	44845	2777
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.2475310874342782	1.109830752610731
Self Consistency Ratio	1.0609122750513307	1.3605742683600222
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	99571	66835

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	82.0	70.0	84.0	84.0
25 percentile	330.0	280.0	336.0	336.0
50 percentile (median)	330.0	280.0	336.0	336.0
75 percentile	330.0	280.0	336.0	336.0
Max size	863.0	502.0	926.0	926.0
Mean	329.20796215765637	279.44988404279195	304.0908500973394	333.7839223993756

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7552289	6954038
Estimated Fragment Length	170	155
Cross-correlation at Estimated Fragment Length	0.681737224078232	0.675781422532557
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6793421	0.6747082
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6721298	0.668192
NSC (Normalized Strand Cross-correlation coeff.)	1.014294	1.011358
RSC (Relative Strand Cross-correlation coeff.)	1.332084	1.164704

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	0.40221545081867416	0.40142276945747934
Synthetic AUC	0.49825521222589597	0.49820738625029015
X-intercept	0.01910276292495215	0.019400152087612046
Synthetic X-intercept	0.0	0.0
Elbow Point	0.573054945142677	0.5566486436858692
Synthetic Elbow Point	0.502577825478586	0.502173165396399
JS Distance	0.07821226994280522	0.06790753646438286
Synthetic JS Distance	0.15133716309185755	0.15095320199368573
% Genome Enriched	37.71293762611596	39.64197538256421
Diff. Enrichment	10.30736191637953	10.237824992151095
CHANCE Divergence	0.08800174268661057	0.08713705527227694

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	0.4809953728189508	0.3375965482442344	0.3396605028780173	0.3454366751354987	0.3340613660023406	0.3475973606217773	0.4754610307617796	0.35543752107225773	0.34738416949458945

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	0.253985218226138	0.1688559011707021	0.15714211684186336	0.2152894877865674

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	0.036203583093881345	0.03632465045534951	0.024755271454986	0.03871084645382909

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