QC Report

	general
Report generated at	2021-08-29 11:40:51
Title	daf-19_OP794_L4larva_1_8
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	23837588	20684902	29763098
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	23658271	20538011	29647673
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.2	99.3	99.6
Paired Reads	23837588	20684902	29763098
Paired Reads (QC-failed)	0	0	0
Read1	11918794	10342451	14881549
Read1 (QC-failed)	0	0	0
Read2	11918794	10342451	14881549
Read2 (QC-failed)	0	0	0
Properly Paired Reads	23577574	20469172	21110528
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.9	99.0	70.89999999999999
With itself	23635086	20521282	29583494
With itself (QC-failed)	0	0	0
Singletons	23185	16729	64179
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.2
Diff. Chroms	9658	8014	5141968
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	10811040	9378350	5868959
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1306955	1043389	754261
Paired Optical Duplicate Reads	61885	48999	33222
% Duplicate Reads	12.0891	11.1255	12.8517

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	19008170	16669922	10229396
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	19008170	16669922	10229396
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	19008170	16669922	10229396
Paired Reads (QC-failed)	0	0	0
Read1	9504085	8334961	5114698
Read1 (QC-failed)	0	0	0
Read2	9504085	8334961	5114698
Read2 (QC-failed)	0	0	0
Properly Paired Reads	19008170	16669922	10229396
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	19008170	16669922	10229396
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	10638255	9229499	5457848
Distinct Fragments	9367532	8214661	4818975
Positions with Two Read	1025824	831286	485632
NRF = Distinct/Total	0.880552	0.890044	0.882944
PBC1 = OneRead/Distinct	0.878155	0.888221	0.886713
PBC2 = OneRead/TwoRead	8.019064	8.777282	8.798947

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	93583	996
N1	81232	408
N2	77313	394
Np	93809	915
N optimal	93809	996
N conservative	93583	996
Optimal Set	pooled-pr1_vs_pooled-pr2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0024149685306092	1.0885245901639344
Self Consistency Ratio	1.0506900521257745	1.0355329949238579
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	119407	119835

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	92.0	86.0	95.0	95.0
25 percentile	360.0	344.0	380.0	380.0
50 percentile (median)	360.0	344.0	380.0	380.0
75 percentile	360.0	344.0	380.0	380.0
Max size	360.0	344.0	380.0	380.0
Mean	359.9732176505565	343.9733717194476	374.0120481927711	379.9364240104894

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	10054290	8718768
Estimated Fragment Length	205	195
Cross-correlation at Estimated Fragment Length	0.758771348504551	0.735335150256322
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7588049	0.7350039
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7549458	0.7312833
NSC (Normalized Strand Cross-correlation coeff.)	1.005067	1.005541
RSC (Relative Strand Cross-correlation coeff.)	0.9913077	1.089033

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	0.4188833186923745	0.4144838609402378
Synthetic AUC	0.49853966173735986	0.4984400481853947
X-intercept	0.01849234111201623	0.018717954861277492
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5258896768731931	0.5274410209720958
Synthetic Elbow Point	0.501338069294594	0.5021853978491017
JS Distance	0.17228008481676277	0.16846510193494132
Synthetic JS Distance	0.13928409090383684	0.14313073978194532
% Genome Enriched	67.20434615937515	66.31107543884869
Diff. Enrichment	4.2762450940589725	4.363340089315226
CHANCE Divergence	0.04177243595071652	0.04246723418782368

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	0.4876909244814204	0.4854541610932553	0.4873296601061901	0.48558289767847773	0.48733744356636577	0.4857467822281091	0.4889709909375199	0.4885180532055298	0.48603848950650047

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	0.41574700799583114	0.373677739624593	0.35425714649414675	0.4164228008605393

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	0.009571812304312685	0.004739435726847981	0.0046382340601233765	0.008959615889773478

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