QC Report

	general
Report generated at	2021-09-01 10:00:11
Title	Y53G8AR.9_RW12264_youngadult_1_4
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	14373648	11609436	13371520
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14303648	11548042	13323709
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.5	99.5	99.6
Paired Reads	14373648	11609436	13371520
Paired Reads (QC-failed)	0	0	0
Read1	7186824	5804718	6685760
Read1 (QC-failed)	0	0	0
Read2	7186824	5804718	6685760
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14235832	11489926	13264002
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.0	99.0	99.2
With itself	14294678	11539524	13316522
With itself (QC-failed)	0	0	0
Singletons	8970	8518	7187
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	3728	3067	21783
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	6530628	5264847	6115051
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	771314	575248	781970
Paired Optical Duplicate Reads	56354	42313	64779
% Duplicate Reads	11.8107	10.9262	12.7876

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	11518628	9379198	10666162
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	11518628	9379198	10666162
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	11518628	9379198	10666162
Paired Reads (QC-failed)	0	0	0
Read1	5759314	4689599	5333081
Read1 (QC-failed)	0	0	0
Read2	5759314	4689599	5333081
Read2 (QC-failed)	0	0	0
Properly Paired Reads	11518628	9379198	10666162
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	11518628	9379198	10666162
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	6483527	5229149	6021281
Distinct Fragments	5724172	4663366	5255164
Positions with Two Read	621833	471933	621514
NRF = Distinct/Total	0.882879	0.891802	0.872765
PBC1 = OneRead/Distinct	0.879938	0.889193	0.868647
PBC2 = OneRead/TwoRead	8.100114	8.786489	7.344777

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	66538	2742
N1	37919	1393
N2	36511	1276
Np	66748	2713
N optimal	66748	2742
N conservative	66538	2742
Optimal Set	pooled-pr1_vs_pooled-pr2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0031560912561244	1.0106892738665685
Self Consistency Ratio	1.0385637205225822	1.091692789968652
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	109986	111731

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	66.0	61.0	80.0	80.0
25 percentile	264.0	244.0	320.0	320.0
50 percentile (median)	264.0	244.0	320.0	320.0
75 percentile	264.0	244.0	320.0	320.0
Max size	1215.0	675.0	1400.0	1400.0
Mean	263.8201680213845	243.8504175206523	306.6232676878191	319.45285251992567

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	6114569	4918795
Estimated Fragment Length	135	120
Cross-correlation at Estimated Fragment Length	0.66141696247685	0.615571691270689
Phantom Peak	50	55
Cross-correlation at Phantom Peak	0.6613881	0.6156872
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6532624	0.6074572
NSC (Normalized Strand Cross-correlation coeff.)	1.012483	1.013358
RSC (Relative Strand Cross-correlation coeff.)	1.003546	0.9859671

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	0.38696676179368045	0.38250182359201024
Synthetic AUC	0.49808399908947254	0.4978637988883801
X-intercept	0.019856633113280595	0.020355543493011264
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5941603537873285	0.5928671780830665
Synthetic Elbow Point	0.4984016391357862	0.49868551791296734
JS Distance	0.08994283071753863	0.09523106782331772
Synthetic JS Distance	0.17359211496099372	0.17774125613729597
% Genome Enriched	37.952711278567605	37.72281337558772
Diff. Enrichment	12.050861820761982	12.753184378958949
CHANCE Divergence	0.1026754795592527	0.10866468036272642

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	0.4753790989690786	0.4752716596877473	0.3971698712728634	0.41831286250426475	0.4084436097771367	0.4118199470402367	0.4590011898845363	0.47740301049467915	0.47556463294934437

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	0.34496047579303224	0.20715045229345022	0.19678729460663907	0.34558752666425685

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	0.03494746295619458	0.020183132921733387	0.019153343388208673	0.03453387926571884

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