QC Report

	general
Report generated at	2023-04-20 15:35:08
Title	nhr-40_RW12341_L4larva_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	14148340	14502796	15202842
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	13395744	12968425	13143015
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	94.69999999999999	89.4	86.5
Paired Reads	14148340	14502796	15202842
Paired Reads (QC-failed)	0	0	0
Read1	7074170	7251398	7601421
Read1 (QC-failed)	0	0	0
Read2	7074170	7251398	7601421
Read2 (QC-failed)	0	0	0
Properly Paired Reads	13268522	12777280	13062806
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	93.8	88.1	85.9
With itself	13384632	12956150	13128716
With itself (QC-failed)	0	0	0
Singletons	11112	12275	14299
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	7568	12495	28623
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	6100350	5870244	6028743
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	974658	958044	988661
Paired Optical Duplicate Reads	61386	63935	68318
% Duplicate Reads	15.9771	16.3203	16.3991

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	10251384	9824400	10080164
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	10251384	9824400	10080164
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	10251384	9824400	10080164
Paired Reads (QC-failed)	0	0	0
Read1	5125692	4912200	5040082
Read1 (QC-failed)	0	0	0
Read2	5125692	4912200	5040082
Read2 (QC-failed)	0	0	0
Properly Paired Reads	10251384	9824400	10080164
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	10251384	9824400	10080164
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	6047192	5810993	5894695
Distinct Fragments	5083680	4863397	4932515
Positions with Two Read	729870	712748	728568
NRF = Distinct/Total	0.840668	0.83693	0.836772
PBC1 = OneRead/Distinct	0.834931	0.830925	0.830094
PBC2 = OneRead/TwoRead	5.815452	5.669774	5.619861

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	78512	1261
N1	50937	599
N2	41896	586
Np	78486	1274
N optimal	78512	1274
N conservative	78512	1261
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0003312692709527	1.0103092783505154
Self Consistency Ratio	1.2157962573992744	1.022184300341297
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	119445	119477

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	86.0	88.0	95.0	95.0
25 percentile	344.0	350.0	380.0	380.0
50 percentile (median)	344.0	350.0	380.0	380.0
75 percentile	344.0	350.0	380.0	380.0
Max size	344.0	350.0	380.0	380.0
Mean	343.94218259449957	349.9332340115671	367.99921507064363	379.8064754432443

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	5746749	5554537
Estimated Fragment Length	180	180
Cross-correlation at Estimated Fragment Length	0.627223943304	0.617567991315776
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6274578	0.6180714
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6233103	0.6139897
NSC (Normalized Strand Cross-correlation coeff.)	1.006279	1.005828
RSC (Relative Strand Cross-correlation coeff.)	0.943605	0.8766599

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	0.4068137568455778	0.4062750024416904
Synthetic AUC	0.4980127046951634	0.4979687944159874
X-intercept	0.018397892594144764	0.018397892594144764
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5372847193119	0.5416033047955457
Synthetic Elbow Point	0.4980479327467679	0.49895747481952296
JS Distance	0.05751577512015015	0.05356379698601942
Synthetic JS Distance	0.14455458262798163	0.1466570698968349
% Genome Enriched	46.12784130595302	44.86180127322437
Diff. Enrichment	8.881317156832752	8.72332315185645
CHANCE Divergence	0.07573681272496059	0.0742663958757665

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	0.5597801233472476	0.5613487846586052	0.5165255735225605	0.4694782378567648	0.49629610987160366	0.4665062497455315	0.5617985828100163	0.5617976363961676	0.5600618137752429

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	0.4091188667899595	0.28782308808254575	0.24667674361793088	0.40895130172749417

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	0.015503504122180234	0.008496413752523562	0.008453340662025162	0.015699810278891224

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