QC Report

	general
Report generated at	2022-05-31 21:45:17
Title	mxl-2_RW12316_L4larva_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	15348742	15190250	18780614
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14854866	14916534	17543247
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	96.8	98.2	93.4
Paired Reads	15348742	15190250	18780614
Paired Reads (QC-failed)	0	0	0
Read1	7674371	7595125	9390307
Read1 (QC-failed)	0	0	0
Read2	7674371	7595125	9390307
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14796244	14854252	17466944
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	96.39999999999999	97.8	93.0
With itself	14844052	14906710	17528798
With itself (QC-failed)	0	0	0
Singletons	10814	9824	14449
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	3884	4162	20627
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	6777410	6803386	8040420
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1015304	1018588	1301404
Paired Optical Duplicate Reads	55852	55727	78515
% Duplicate Reads	14.980699999999999	14.971799999999998	16.1858

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	11524212	11569596	13478032
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	11524212	11569596	13478032
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	11524212	11569596	13478032
Paired Reads (QC-failed)	0	0	0
Read1	5762106	5784798	6739016
Read1 (QC-failed)	0	0	0
Read2	5762106	5784798	6739016
Read2 (QC-failed)	0	0	0
Properly Paired Reads	11524212	11569596	13478032
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	11524212	11569596	13478032
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	6737746	6757842	7943489
Distinct Fragments	5731667	5750946	6662222
Positions with Two Read	772576	777135	975564
NRF = Distinct/Total	0.85068	0.851003	0.838702
PBC1 = OneRead/Distinct	0.84614	0.846139	0.831991
PBC2 = OneRead/TwoRead	6.277434	6.261589	5.681749

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	68638	1009
N1	38681	452
N2	36387	457
Np	66616	983
N optimal	68638	1009
N conservative	68638	1009
Optimal Set	rep1_vs_rep2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0303530683319322	1.0264496439471007
Self Consistency Ratio	1.063044493912661	1.011061946902655
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	129504	109894

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	60.0	66.0	65.0	65.0
25 percentile	240.0	244.0	260.0	260.0
50 percentile (median)	240.0	244.0	260.0	260.0
75 percentile	240.0	244.0	260.0	260.0
Max size	412.0	379.0	469.0	469.0
Mean	239.9710433654559	243.97035324949496	254.25966303270565	259.9137649698418

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	6350422	6379097
Estimated Fragment Length	160	160
Cross-correlation at Estimated Fragment Length	0.655615586800617	0.657039061948679
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6553722	0.656548
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6502919	0.6514796
NSC (Normalized Strand Cross-correlation coeff.)	1.008187	1.008534
RSC (Relative Strand Cross-correlation coeff.)	1.047907	1.096878

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	0.4099169117710638	0.4093516856181763
Synthetic AUC	0.49811097966665074	0.49811635803444926
X-intercept	0.019585970737781466	0.01965980475890199
Synthetic X-intercept	0.0	0.0
Elbow Point	0.512725393315826	0.5156847407028999
Synthetic Elbow Point	0.5025240959499493	0.49890585339861915
JS Distance	0.048111350702257034	0.04658524126380156
Synthetic JS Distance	0.13660676432887348	0.1382923076193169
% Genome Enriched	44.24932751175358	44.39779375962836
Diff. Enrichment	9.028530281825574	9.060133429530188
CHANCE Divergence	0.07678186188705499	0.07706239786671744

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	0.515461968245638	0.457650293061227	0.4234496900959476	0.41545582058353636	0.41298233666648965	0.4026233932455377	0.5376041924311487	0.46904027261333425	0.47848263049558565

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	0.29733623835445416	0.18173537591984598	0.17410945032134226	0.29002436497263684

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	0.010963674765114527	0.0064059911428217394	0.006608182342754233	0.01081428407129738

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