QC Report

	general
Report generated at	2021-08-29 12:37:29
Title	egl-44_RW12173_youngadult_1_7
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	15141622	11778470	13184434
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14861868	11486160	13167192
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	98.2	97.5	99.9
Paired Reads	15141622	11778470	13184434
Paired Reads (QC-failed)	0	0	0
Read1	7570811	5889235	6592217
Read1 (QC-failed)	0	0	0
Read2	7570811	5889235	6592217
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14795958	11435350	13021768
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	97.7	97.1	98.8
With itself	14850800	11476944	13158746
With itself (QC-failed)	0	0	0
Singletons	11068	9216	8446
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	4511	3457	64733
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	6751984	5212484	5898475
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1260361	953527	900027
Paired Optical Duplicate Reads	75978	58246	58412
% Duplicate Reads	18.6665	18.293100000000003	15.2586

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	10983246	8517914	9996896
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	10983246	8517914	9996896
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	10983246	8517914	9996896
Paired Reads (QC-failed)	0	0	0
Read1	5491623	4258957	4998448
Read1 (QC-failed)	0	0	0
Read2	5491623	4258957	4998448
Read2 (QC-failed)	0	0	0
Properly Paired Reads	10983246	8517914	9996896
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	10983246	8517914	9996896
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	6685544	5150851	5837425
Distinct Fragments	5443609	4214926	4950459
Positions with Two Read	882662	671451	679463
NRF = Distinct/Total	0.814236	0.818297	0.848055
PBC1 = OneRead/Distinct	0.807506	0.811753	0.843123
PBC2 = OneRead/TwoRead	4.980103	5.09565	6.142857

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	53597	1442
N1	34096	769
N2	29281	568
Np	55738	1553
N optimal	55738	1553
N conservative	53597	1442
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0399462656491967	1.0769764216366158
Self Consistency Ratio	1.1644411051535126	1.3538732394366197
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	109962	80175

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	72.0	69.0	78.0	78.0
25 percentile	290.0	270.0	310.0	310.0
50 percentile (median)	290.0	270.0	310.0	310.0
75 percentile	290.0	270.0	310.0	310.0
Max size	290.0	289.0	310.0	310.0
Mean	289.9634601043997	269.96347988774556	302.3663876368319	309.7873084789551

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	6305281	4859131
Estimated Fragment Length	185	160
Cross-correlation at Estimated Fragment Length	0.636910993887062	0.575861757623781
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6359779	0.575575
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6314056	0.5709912
NSC (Normalized Strand Cross-correlation coeff.)	1.008719	1.00853
RSC (Relative Strand Cross-correlation coeff.)	1.204078	1.06256

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	0.39481655325266507	0.39067075644216026
Synthetic AUC	0.49807417984983143	0.4978093304427261
X-intercept	0.019013204889280853	0.01943022239603494
Synthetic X-intercept	0.0	0.0
Elbow Point	0.54898459230054	0.5474202778254432
Synthetic Elbow Point	0.4997888380764194	0.49788606889327447
JS Distance	0.05330828148727697	0.05772529434890021
Synthetic JS Distance	0.15930002226050033	0.16554004560149294
% Genome Enriched	40.26932546919458	41.63331191712326
Diff. Enrichment	11.427673102733454	11.89182832445304
CHANCE Divergence	0.09720016905494987	0.10112245942957833

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	0.49751812897571446	0.3994020132159118	0.3977102219671267	0.39889780551956605	0.39954170188698346	0.40171253236708715	0.49184827979463785	0.4648474316712582	0.440722078219363

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	0.28144807796049054	0.19503532926422662	0.17363194791588646	0.2960075708316839

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	0.01571055260302464	0.009704690216353161	0.01397666142203361	0.021846341448406147

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