QC Report

	general
Report generated at	2022-06-01 01:37:48
Title	madf-9_RW12324_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	16390724	14743124	16169714
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	16324829	14652049	16084442
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.6	99.4	99.5
Paired Reads	16390724	14743124	16169714
Paired Reads (QC-failed)	0	0	0
Read1	8195362	7371562	8084857
Read1 (QC-failed)	0	0	0
Read2	8195362	7371562	8084857
Read2 (QC-failed)	0	0	0
Properly Paired Reads	16266886	14592090	16017222
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.2	99.0	99.1
With itself	16313384	14643876	16075070
With itself (QC-failed)	0	0	0
Singletons	11445	8173	9372
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	3992	3324	18704
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	7469705	6690061	7375606
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1054103	977895	1021308
Paired Optical Duplicate Reads	55269	49756	65179
% Duplicate Reads	14.111699999999999	14.617099999999999	13.847100000000001

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	12831204	11424332	12708596
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	12831204	11424332	12708596
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	12831204	11424332	12708596
Paired Reads (QC-failed)	0	0	0
Read1	6415602	5712166	6354298
Read1 (QC-failed)	0	0	0
Read2	6415602	5712166	6354298
Read2 (QC-failed)	0	0	0
Properly Paired Reads	12831204	11424332	12708596
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	12831204	11424332	12708596
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	7417198	6638574	7276393
Distinct Fragments	6376871	5674956	6272384
Positions with Two Read	816528	745160	803087
NRF = Distinct/Total	0.859741	0.854846	0.862018
PBC1 = OneRead/Distinct	0.855459	0.850637	0.856806
PBC2 = OneRead/TwoRead	6.680909	6.478246	6.69195

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	64254	1637
N1	34227	1002
N2	35140	806
Np	54637	1632
N optimal	64254	1637
N conservative	64254	1637
Optimal Set	rep1_vs_rep2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.176016252722514	1.0030637254901962
Self Consistency Ratio	1.0266748473427412	1.2431761786600497
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	135073	96823

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	61.0	58.0	65.0	65.0
25 percentile	244.0	230.0	260.0	260.0
50 percentile (median)	244.0	230.0	260.0	260.0
75 percentile	244.0	230.0	260.0	260.0
Max size	364.0	282.0	434.0	434.0
Mean	243.9174742546623	229.9407682059015	248.1905925473427	259.70159056245524

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7001094	6263761
Estimated Fragment Length	140	145
Cross-correlation at Estimated Fragment Length	0.681614997717508	0.654779432589648
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6813514	0.6547409
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6760583	0.6496478
NSC (Normalized Strand Cross-correlation coeff.)	1.008219	1.007899
RSC (Relative Strand Cross-correlation coeff.)	1.049804	1.007564

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	0.4069408736286277	0.40535978998716915
Synthetic AUC	0.49821282849000614	0.4980975465636365
X-intercept	0.019465822542272748	0.019769196378674418
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5340078078845263	0.5306367657155631
Synthetic Elbow Point	0.5001105742808679	0.4983593303009034
JS Distance	0.053427233142468535	0.05206580128175339
Synthetic JS Distance	0.1428072384759444	0.14444571199044584
% Genome Enriched	43.01302112439924	43.41279598907854
Diff. Enrichment	9.11452462574765	9.380068303377726
CHANCE Divergence	0.07747532161037864	0.07975321816780181

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	0.5332477762803864	0.40270389551003943	0.3820925924020848	0.401470650537817	0.38095988498039624	0.387182725431999	0.5229692718396328	0.4202373429307025	0.41747170625295604

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	0.283710860893777	0.16904313889795533	0.16666996372304307	0.24834940773933012

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	0.016795464754932647	0.011981260682941367	0.009742976657190984	0.016672729887313147

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