QC Report

	general
Report generated at	2021-08-30 23:37:38
Title	madf-3_RW12241_youngadult_1_3
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	18604618	17557082	13217810
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	18471634	17486342	13189198
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.3	99.6	99.8
Paired Reads	18604618	17557082	13217810
Paired Reads (QC-failed)	0	0	0
Read1	9302309	8778541	6608905
Read1 (QC-failed)	0	0	0
Read2	9302309	8778541	6608905
Read2 (QC-failed)	0	0	0
Properly Paired Reads	18373518	17437042	13126382
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.8	99.3	99.3
With itself	18463042	17480360	13182746
With itself (QC-failed)	0	0	0
Singletons	8592	5982	6452
Singletons (QC-failed)	0	0	0
% Singleton	0.0	0.0	0.0
Diff. Chroms	3016	2466	22931
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	8368439	7945826	6047886
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	933704	864172	668900
Paired Optical Duplicate Reads	45888	47744	54293
% Duplicate Reads	11.1574	10.8758	11.0601

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	14869470	14163308	10757972
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14869470	14163308	10757972
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	14869470	14163308	10757972
Paired Reads (QC-failed)	0	0	0
Read1	7434735	7081654	5378986
Read1 (QC-failed)	0	0	0
Read2	7434735	7081654	5378986
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14869470	14163308	10757972
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	14869470	14163308	10757972
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	8309448	7891258	5970383
Distinct Fragments	7400542	7041166	5313551
Positions with Two Read	747291	707382	546532
NRF = Distinct/Total	0.890618	0.892274	0.889985
PBC1 = OneRead/Distinct	0.888685	0.889919	0.88723
PBC2 = OneRead/TwoRead	8.800791	8.858111	8.625925

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	91530	2631
N1	55960	962
N2	57330	863
Np	91160	2741
N optimal	91530	2741
N conservative	91530	2631
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0040587977182975	1.041809198023565
Self Consistency Ratio	1.024481772694782	1.1147161066048668
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	150668	145503

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	50.0	52.0	55.0	55.0
25 percentile	190.0	204.0	220.0	220.0
50 percentile (median)	190.0	204.0	220.0	220.0
75 percentile	190.0	204.0	220.0	220.0
Max size	353.0	335.0	372.0	372.0
Mean	189.96369501154857	203.95483254640797	215.55052900401313	219.86486397902328

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7812580	7427407
Estimated Fragment Length	110	125
Cross-correlation at Estimated Fragment Length	0.717349992824091	0.706620090241663
Phantom Peak	55	55
Cross-correlation at Phantom Peak	0.7161939	0.7052506
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.708994	0.6988638
NSC (Normalized Strand Cross-correlation coeff.)	1.011786	1.011098
RSC (Relative Strand Cross-correlation coeff.)	1.160569	1.214428

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	0.40110400196113283	0.40221798498809797
Synthetic AUC	0.49828522684917875	0.4982712963421215
X-intercept	0.02020274599268294	0.019937288057786003
Synthetic X-intercept	0.0	0.0
Elbow Point	0.533520551034787	0.5212496082998517
Synthetic Elbow Point	0.5015791201634799	0.49861103863756573
JS Distance	0.05917999324271022	0.055706621098974694
Synthetic JS Distance	0.15143487303493894	0.14937259854476084
% Genome Enriched	42.45590504190443	42.99220990736915
Diff. Enrichment	10.544617684248076	10.398553722717912
CHANCE Divergence	0.08964261071054126	0.08840819453678926

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	0.5031144351479911	0.5134615444358055	0.4467607188742142	0.46280995936824926	0.43859847574909877	0.46285627623151315	0.4914901701793745	0.5085311844060404	0.5088253358893411

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	0.3436286393262126	0.21828767266082785	0.23266181883497838	0.3422849511679523

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	0.022202353491629356	0.011870631569248937	0.010657750293928509	0.02283711879035482

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