QC Report

	general
Report generated at	2021-09-01 14:01:47
Title	Y79H2A.3_RW12273_youngadult_1_3
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	12600192	16527746	15147654
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	12567877	16495476	15120404
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.7	99.8	99.8
Paired Reads	12600192	16527746	15147654
Paired Reads (QC-failed)	0	0	0
Read1	6300096	8263873	7573827
Read1 (QC-failed)	0	0	0
Read2	6300096	8263873	7573827
Read2 (QC-failed)	0	0	0
Properly Paired Reads	12510130	16436730	15008878
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.3	99.4	99.1
With itself	12555874	16481974	15107874
With itself (QC-failed)	0	0	0
Singletons	12003	13502	12530
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	9145	8185	18654
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	5642357	7487566	6770611
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	801995	1279632	1107506
Paired Optical Duplicate Reads	45033	76906	69192
% Duplicate Reads	14.213799999999999	17.0901	16.357499999999998

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	9680724	12415868	11326210
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	9680724	12415868	11326210
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	9680724	12415868	11326210
Paired Reads (QC-failed)	0	0	0
Read1	4840362	6207934	5663105
Read1 (QC-failed)	0	0	0
Read2	4840362	6207934	5663105
Read2 (QC-failed)	0	0	0
Properly Paired Reads	9680724	12415868	11326210
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	9680724	12415868	11326210
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	5612632	7444705	6725335
Distinct Fragments	4820422	6179439	5631975
Positions with Two Read	611289	931055	812128
NRF = Distinct/Total	0.858852	0.830045	0.837427
PBC1 = OneRead/Distinct	0.855578	0.824182	0.832551
PBC2 = OneRead/TwoRead	6.746801	5.470118	5.773605

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	53421	1021
N1	28292	442
N2	29976	393
Np	40280	934
N optimal	53421	1021
N conservative	53421	1021
Optimal Set	rep1_vs_rep2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.3262413108242304	1.0931477516059958
Self Consistency Ratio	1.0595221263961543	1.1246819338422391
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	74957	130212

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	71.0	67.0	74.0	74.0
25 percentile	280.0	264.0	296.0	296.0
50 percentile (median)	280.0	264.0	296.0	296.0
75 percentile	280.0	264.0	296.0	296.0
Max size	280.0	264.0	296.0	296.0
Mean	279.9622049975319	263.9802936749301	288.8570029382958	295.8589693191816

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	5255898	6979713
Estimated Fragment Length	190	160
Cross-correlation at Estimated Fragment Length	0.612478525051785	0.664703490106367
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6127647	0.6646279
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6079878	0.6602982
NSC (Normalized Strand Cross-correlation coeff.)	1.007386	1.006672
RSC (Relative Strand Cross-correlation coeff.)	0.9400978	1.01745

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	0.39970877118582676	0.408499628621071
Synthetic AUC	0.4979512845572517	0.4981914627232132
X-intercept	0.019570623904703738	0.019323121878779895
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5407160792485519	0.5282591426050786
Synthetic Elbow Point	0.5007568287892876	0.49960583975635403
JS Distance	0.05087628096443426	0.03680539359249907
Synthetic JS Distance	0.14794943115822057	0.13758568998359216
% Genome Enriched	41.40110098481855	41.38453431695429
Diff. Enrichment	10.191287710393148	8.921997509414597
CHANCE Divergence	0.08663316337171519	0.07583996100584715

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	0.3712388660186986	0.5358948725936842	0.3837648919646919	0.3611128919862872	0.384405339931187	0.37294082056929084	0.5305334867928955	0.371654235187037	0.364935190005771

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	0.26172162657481296	0.15982502961555356	0.15443503426421737	0.2071114857893018

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	0.010927884263781492	0.0062332114829428045	0.004866594909030927	0.01011115198216992

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