QC Report

	general
Report generated at	2024-05-06 12:41:47
Title	end-1_RW12352_lateembryonic_1_4
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	12986386	13137052	13124372
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	10522874	10578100	13103093
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	81.0	80.5	99.8
Paired Reads	12986386	13137052	13124372
Paired Reads (QC-failed)	0	0	0
Read1	6493193	6568526	6562186
Read1 (QC-failed)	0	0	0
Read2	6493193	6568526	6562186
Read2 (QC-failed)	0	0	0
Properly Paired Reads	10377664	10408802	13039874
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	79.9	79.2	99.4
With itself	10503894	10557594	13092560
With itself (QC-failed)	0	0	0
Singletons	18980	20506	10533
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.2	0.1
Diff. Chroms	22169	31190	11056
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	4527059	4531942	5995129
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	719049	724581	587792
Paired Optical Duplicate Reads	308856	290835	462676
% Duplicate Reads	15.8834	15.988299999999999	9.804499999999999

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	7616020	7614722	10814674
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	7616020	7614722	10814674
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	7616020	7614722	10814674
Paired Reads (QC-failed)	0	0	0
Read1	3808010	3807361	5407337
Read1 (QC-failed)	0	0	0
Read2	3808010	3807361	5407337
Read2 (QC-failed)	0	0	0
Properly Paired Reads	7616020	7614722	10814674
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	7616020	7614722	10814674
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	4523980	4524374	5928253
Distinct Fragments	3811720	3806861	5353307
Positions with Two Read	503975	508600	444931
NRF = Distinct/Total	0.842559	0.841412	0.903016
PBC1 = OneRead/Distinct	0.843095	0.841594	0.905724
PBC2 = OneRead/TwoRead	6.37659	6.299314	10.897458

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	23266	11993
N1	25372	13452
N2	23741	11201
Np	24953	14465
N optimal	24953	14465
N conservative	23266	11993
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0725092409524628	1.2061202368048027
Self Consistency Ratio	1.0686997177877933	1.2009641996250335
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	28630	31750

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	98.0	100.0	101.0	101.0
25 percentile	238.0	400.0	220.0	260.0
50 percentile (median)	390.0	400.0	305.0	404.0
75 percentile	390.0	400.0	404.0	404.0
Max size	2154.0	1789.0	3437.0	3437.0
Mean	343.5487600419141	370.12343307086616	353.06947805046667	368.03125876648096

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	4172886	4197139
Estimated Fragment Length	215	215
Cross-correlation at Estimated Fragment Length	0.620553813437308	0.593016625656254
Phantom Peak	55	55
Cross-correlation at Phantom Peak	0.5209368	0.5423295
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.4664242	0.5090504
NSC (Normalized Strand Cross-correlation coeff.)	1.330449	1.164947
RSC (Relative Strand Cross-correlation coeff.)	2.827411	2.523095

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	0.1573329173118111	0.25699168751617396
Synthetic AUC	0.49767109969303264	0.49767631689808073
X-intercept	0.027966056039858016	0.020270202861652223
Synthetic X-intercept	0.0	0.0
Elbow Point	0.7707146548438781	0.747523339964364
Synthetic Elbow Point	0.5032111027441083	0.49853873120045333
JS Distance	0.46306306513211365	0.29834113076829566
Synthetic JS Distance	0.5260509818043666	0.3648789929494198
% Genome Enriched	22.61327789073365	23.911217349489903
Diff. Enrichment	53.24553948524151	33.67184947220427
CHANCE Divergence	0.4642631297288133	0.2923992818047382

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	0.5481444376459096	0.4194847822415579	0.5484688853233054	0.44857305399381514	0.5470166832545083	0.4464747226424609	0.4710445492412648	0.4729160965478771	0.473394201463619

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	0.43426347843066343	0.5213587937006467	0.3722728157377249	0.4489720855359509

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	0.3224543492365638	0.38840365440216806	0.2640759570736791	0.3584622469476536

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