QC Report

	general
Report generated at	2022-12-27 10:32:40
Title	mml-1_OP198_L3larva_1_1
Description	ENCSR746LWS
Pipeline version	v1.3.6
Pipeline type	tf
Genome	WS245chr
Aligner	bwa
Sequencing endedness	{'rep1': {'paired_end': False}, 'rep2': {'paired_end': False}, 'rep3': {'paired_end': False}, 'ctl1': {'paired_end': False}}
Peak caller	spp

Alignment quality metrics

Marking duplicates (filtered BAM)

	rep1	rep2	rep3	ctl1
Unpaired Reads	1613679	1329058	844601	6939376
Paired Reads	0	0	0	0
Unmapped Reads	0	0	0	0
Unpaired Duplicate Reads	57602	36150	10847	303920
Paired Duplicate Reads	0	0	0	0
Paired Optical Duplicate Reads	0	0	0	0
% Duplicate Reads	3.5696	2.7199999999999998	1.2843	4.3796

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	rep3	ctl1
Total Reads	1556077	1292908	833754	6635456
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	1556077	1292908	833754	6635456
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0
Paired Reads	0	0	0	0
Paired Reads (QC-failed)	0	0	0	0
Read1	0	0	0	0
Read1 (QC-failed)	0	0	0	0
Read2	0	0	0	0
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	0	0	0	0
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	0.0	0.0	0.0	0.0
With itself	0	0	0	0
With itself (QC-failed)	0	0	0	0
Singletons	0	0	0	0
Singletons (QC-failed)	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0
Diff. Chroms (QC-failed)	0	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	rep3	ctl1
Total Fragments	1610501	1327843	842828	6877656
Distinct Fragments	1553354	1291833	832081	6614170
Positions with Two Read	48215	30798	9491	209487
NRF = Distinct/Total	0.964516	0.972881	0.987249	0.96169
PBC1 = OneRead/Distinct	0.966892	0.974718	0.987942	0.966006
PBC2 = OneRead/TwoRead	31.150576	40.884895	86.613423	30.499878

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	8710	138
N1	4219	84
N2	4478	41
N3	2344	93
Np	8619	120
N optimal	8710	138
N conservative	8710	138
Optimal Set	rep1_vs_rep2	rep1_vs_rep3
Conservative Set	rep1_vs_rep2	rep1_vs_rep3
Rescue Ratio	1.0105580693815988	1.15
Self Consistency Ratio	1.9104095563139931	2.268292682926829
Reproducibility Test	pass	borderline

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	rep3
Number of peaks	38879	37627	29489

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	rep3	idr_opt	overlap_opt
Min size	137.0	138.0	142.0	118.0	118.0
25 percentile	396.0	476.0	570.0	315.75	460.0
50 percentile (median)	396.0	476.0	570.0	460.0	460.0
75 percentile	396.0	476.0	570.0	460.0	460.0
Max size	396.0	476.0	570.0	489.0	489.0
Mean	395.90151495666044	475.8836473808701	569.6915799111533	390.78985507246375	458.7769230769231

Enrichment / Signal-to-noise ratio

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

	rep1	rep2	rep3
Number of Subsampled Reads	1610501	1327843	842828
Estimated Fragment Length	100	90	125
Cross-correlation at Estimated Fragment Length	0.389241415433848	0.348392062108628	0.264219627603945
Phantom Peak	35	35	30
Cross-correlation at Phantom Peak	0.3863804	0.3457906	0.2626764
Argmin of Cross-correlation	1500	1500	1500
Minimum of Cross-correlation	0.3773737	0.3379311	0.2519105
NSC (Normalized Strand Cross-correlation coeff.)	1.031448	1.030956	1.048863
RSC (Relative Strand Cross-correlation coeff.)	1.31765	1.330997	1.14334

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	rep3
AUC	0.35667940804974674	0.34959868864083615	0.3272860661551038
Synthetic AUC	0.49101800373546983	0.49014571344799424	0.4877179841843579
X-intercept	0.04776099747996241	0.05272724733281057	0.07014403920324512
Synthetic X-intercept	1.6050479184422138e-105	1.8034095017981383e-87	6.060019212958625e-56
Elbow Point	0.5015034428542069	0.5165598194671407	0.5697260282172381
Synthetic Elbow Point	0.4963374811961531	0.5167979510831432	0.5219587282939029
JS Distance	0.07869043341503368	0.08664925365430318	0.11764755954301145
Synthetic JS Distance	0.17587628814739503	0.17972208493504133	0.1979887367828878
% Genome Enriched	39.93970266349816	41.74143975354312	40.27730389897503
Diff. Enrichment	13.59631077800762	14.793118753110685	18.824118286509606
CHANCE Divergence	0.115810339939804	0.12652852246126298	0.1611797924752246

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for spp raw peaks

	rep1	rep2	rep3	rep1-pr1	rep2-pr1	rep3-pr1	rep1-pr2	rep2-pr2	rep3-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.23993028622619575	0.2551302954270528	0.24852414501159814	0.19892061966045405	0.2039186082845802	0.1722258603856773	0.18319413704729076	0.20272749491843195	0.1642882672826757	0.21048165509421113	0.23282881767379723	0.23430610594617374

FRiP for overlap peaks

	rep1_vs_rep2	rep1_vs_rep3	rep2_vs_rep3	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	rep3-pr1_vs_rep3-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.06423887220897273	0.05212777772196183	0.046462157649510324	0.03641657835698362	0.036982523118427604	0.030721291891852992	0.061385018053139256

FRiP for IDR peaks

	rep1_vs_rep2	rep1_vs_rep3	rep2_vs_rep3	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	rep3-pr1_vs_rep3-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.004008972669526676	0.004831729861931568	0.0037789808074913805	0.003612931750806676	0.001823795660634786	0.005740302295401282	0.0045512321128377544

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