QC Report

	general
Report generated at	2022-07-25 11:28:48
Title	ceh-37_OH16345_L1larva_1_1
Description	mkudron
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	16995622	15381820	13711110
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	16903814	15242233	13542901
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.5	99.1	98.8
Paired Reads	16995622	15381820	13711110
Paired Reads (QC-failed)	0	0	0
Read1	8497811	7690910	6855555
Read1 (QC-failed)	0	0	0
Read2	8497811	7690910	6855555
Read2 (QC-failed)	0	0	0
Properly Paired Reads	16831034	15167476	13443014
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.0	98.6	98.0
With itself	16880868	15215348	13519190
With itself (QC-failed)	0	0	0
Singletons	22946	26885	23711
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.2	0.2
Diff. Chroms	9163	11120	9893
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	7757584	6976333	6221134
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1308667	1116164	876960
Paired Optical Duplicate Reads	90366	70828	62934
% Duplicate Reads	16.869500000000002	15.9993	14.0965

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	12897834	11720338	10688348
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	12897834	11720338	10688348
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	12897834	11720338	10688348
Paired Reads (QC-failed)	0	0	0
Read1	6448917	5860169	5344174
Read1 (QC-failed)	0	0	0
Read2	6448917	5860169	5344174
Read2 (QC-failed)	0	0	0
Properly Paired Reads	12897834	11720338	10688348
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	12897834	11720338	10688348
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	7714833	6938433	6088106
Distinct Fragments	6423704	5840150	5244245
Positions with Two Read	949812	822608	660237
NRF = Distinct/Total	0.832643	0.84171	0.861392
PBC1 = OneRead/Distinct	0.827449	0.837118	0.8576
PBC2 = OneRead/TwoRead	5.596144	5.943165	6.811892

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	88284	1026
N1	69268	633
N2	67102	523
Np	89421	1019
N optimal	89421	1026
N conservative	88284	1026
Optimal Set	pooled-pr1_vs_pooled-pr2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0128788908522495	1.0068694798822375
Self Consistency Ratio	1.032279216714852	1.2103250478011471
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	130601	135177

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	82.0	83.0	88.0	88.0
25 percentile	330.0	320.0	350.0	350.0
50 percentile (median)	330.0	320.0	350.0	350.0
75 percentile	330.0	320.0	350.0	350.0
Max size	342.0	320.0	457.0	457.0
Mean	329.8968767467324	319.9357656997862	333.0711500974659	349.80503461155655

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7252749	6529433
Estimated Fragment Length	180	175
Cross-correlation at Estimated Fragment Length	0.675782918042234	0.654736360695663
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6753678	0.6545602
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6710619	0.6505569
NSC (Normalized Strand Cross-correlation coeff.)	1.007035	1.006424
RSC (Relative Strand Cross-correlation coeff.)	1.096395	1.044

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	0.4117990091782905	0.4125224167029383
Synthetic AUC	0.49822887690207746	0.4981415329045851
X-intercept	0.018611788463764184	0.018739498816683763
Synthetic X-intercept	0.0	0.0
Elbow Point	0.536858405137149	0.528501358917974
Synthetic Elbow Point	0.5001540717510727	0.501108298351597
JS Distance	0.06425032911292149	0.06351843231727193
Synthetic JS Distance	0.13548246580558823	0.13347348823717767
% Genome Enriched	47.4553712180774	48.09531981466035
Diff. Enrichment	5.451278865020476	4.943785115892468
CHANCE Divergence	0.046699459767421334	0.042448579812540715

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	0.5740149082396315	0.5868666074306048	0.5679817916742003	0.572019241762611	0.567910793069719	0.5720475931748031	0.5830604319443377	0.5803373897400035	0.5813318846471435

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	0.41775412894182395	0.34662882155251806	0.33118490268796	0.42282664204312165

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	0.013285592447725201	0.009742798674568148	0.007841582725685898	0.01330041889381551

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