QC Report

	general
Report generated at	2021-08-31 00:36:30
Title	madf-6_RW12237_youngadult_1_6
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	13839202	26032060	15887766
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	13537612	25863674	15852657
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	97.8	99.4	99.8
Paired Reads	13839202	26032060	15887766
Paired Reads (QC-failed)	0	0	0
Read1	6919601	13016030	7943883
Read1 (QC-failed)	0	0	0
Read2	6919601	13016030	7943883
Read2 (QC-failed)	0	0	0
Properly Paired Reads	13404534	25793432	15790006
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	96.89999999999999	99.1	99.4
With itself	13527976	25853456	15843530
With itself (QC-failed)	0	0	0
Singletons	9636	10218	9127
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.0	0.1
Diff. Chroms	3749	3634	14480
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	6144259	11807540	7271502
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1214495	1631775	1193100
Paired Optical Duplicate Reads	73082	81400	80886
% Duplicate Reads	19.7663	13.819799999999999	16.4079

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	9859528	20351530	12156804
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	9859528	20351530	12156804
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	9859528	20351530	12156804
Paired Reads (QC-failed)	0	0	0
Read1	4929764	10175765	6078402
Read1 (QC-failed)	0	0	0
Read2	4929764	10175765	6078402
Read2 (QC-failed)	0	0	0
Properly Paired Reads	9859528	20351530	12156804
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	9859528	20351530	12156804
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	6035830	11598143	7136728
Distinct Fragments	4853043	10048937	5976748
Positions with Two Read	825508	1212078	869689
NRF = Distinct/Total	0.804039	0.866426	0.837463
PBC1 = OneRead/Distinct	0.796156	0.863827	0.831784
PBC2 = OneRead/TwoRead	4.680488	7.161703	5.716254

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	48075	4384
N1	38609	2803
N2	50672	4519
Np	51099	5060
N optimal	51099	5060
N conservative	48075	4384
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0629017160686427	1.1541970802919708
Self Consistency Ratio	1.3124401046388148	1.6122012129860863
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	81427	79710

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	78.0	68.0	80.0	80.0
25 percentile	310.0	270.0	220.75	320.0
50 percentile (median)	310.0	270.0	320.0	320.0
75 percentile	310.0	270.0	320.0	320.0
Max size	642.0	738.0	838.0	838.0
Mean	308.4362189445761	267.86854848827	276.74604743083006	315.71637409734046

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	5721452	10919909
Estimated Fragment Length	155	130
Cross-correlation at Estimated Fragment Length	0.614215386610206	0.770508925938889
Phantom Peak	50	55
Cross-correlation at Phantom Peak	0.6036877	0.7613013
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.5926205	0.7453621
NSC (Normalized Strand Cross-correlation coeff.)	1.03644	1.033738
RSC (Relative Strand Cross-correlation coeff.)	1.95125	1.577674

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	0.367614117780823	0.3671900320378541
Synthetic AUC	0.4979667727597876	0.4985642366892922
X-intercept	0.01964625556906843	0.019592337201476965
Synthetic X-intercept	0.0	0.0
Elbow Point	0.6361668433990938	0.6592518926345513
Synthetic Elbow Point	0.5013211094188368	0.4985175934449144
JS Distance	0.11703129138522274	0.1267909646909327
Synthetic JS Distance	0.21111475399183768	0.21550489222440292
% Genome Enriched	34.2505446753615	31.522474972891043
Diff. Enrichment	14.98628311039698	14.891916056441124
CHANCE Divergence	0.1283527769957171	0.12854496762031323

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	0.43166305729848325	0.3858162015337422	0.4493679616306176	0.41431161054607585	0.4500335107319539	0.4132829731507138	0.37926453949411504	0.39670200251166293	0.399214843731381

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	0.2872637893052272	0.2605821495714602	0.2821577050963736	0.30089591698509865

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	0.07110747329669818	0.060412932546061025	0.07147998209471229	0.07653561818324933

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