QC Report

	general
Report generated at	2021-08-27 18:17:57
Title	attf-6_RW12231_youngadult_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	14548426	14326678	18557606
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14371437	14260381	18492908
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	98.8	99.5	99.7
Paired Reads	14548426	14326678	18557606
Paired Reads (QC-failed)	0	0	0
Read1	7274213	7163339	9278803
Read1 (QC-failed)	0	0	0
Read2	7274213	7163339	9278803
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14323444	14203510	18413008
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.5	99.1	99.2
With itself	14359968	14249666	18480892
With itself (QC-failed)	0	0	0
Singletons	11469	10715	12016
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	5356	4968	23680
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	6260036	6244521	8471208
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	699859	745854	1185849
Paired Optical Duplicate Reads	42900	45325	80905
% Duplicate Reads	11.1798	11.9441	13.9986

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	11120354	10997334	14570718
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	11120354	10997334	14570718
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	11120354	10997334	14570718
Paired Reads (QC-failed)	0	0	0
Read1	5560177	5498667	7285359
Read1 (QC-failed)	0	0	0
Read2	5560177	5498667	7285359
Read2 (QC-failed)	0	0	0
Properly Paired Reads	11120354	10997334	14570718
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	11120354	10997334	14570718
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	6209675	6196092	8366263
Distinct Fragments	5518840	5462047	7200757
Positions with Two Read	573479	600902	925649
NRF = Distinct/Total	0.888749	0.881531	0.86069
PBC1 = OneRead/Distinct	0.885978	0.878405	0.855654
PBC2 = OneRead/TwoRead	8.526152	7.98448	6.656256

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	55134	2134
N1	29723	1219
N2	31254	1110
Np	60151	2269
N optimal	60151	2269
N conservative	55134	2134
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0909964813001052	1.063261480787254
Self Consistency Ratio	1.0515089324765334	1.0981981981981983
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	106658	88182

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	76.0	68.0	81.0	81.0
25 percentile	304.0	270.0	324.0	324.0
50 percentile (median)	304.0	270.0	324.0	324.0
75 percentile	304.0	270.0	324.0	324.0
Max size	1575.0	1648.0	1699.0	1699.0
Mean	303.9029702413321	269.9452722777891	320.33142353459675	323.8669182557231

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	5831465	5815421
Estimated Fragment Length	135	125
Cross-correlation at Estimated Fragment Length	0.6518656728163	0.648206529958199
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6520072	0.6484494
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6426176	0.6387567
NSC (Normalized Strand Cross-correlation coeff.)	1.014391	1.014794
RSC (Relative Strand Cross-correlation coeff.)	0.9849236	0.9749386

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	0.39345418271370436	0.39388554863360964
Synthetic AUC	0.49807105373751714	0.4980392397358241
X-intercept	0.019721160871492054	0.019978679826084873
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5713467243189722	0.565341941253738
Synthetic Elbow Point	0.5013258906656667	0.4992822674645325
JS Distance	0.0859456740321949	0.08516159465823189
Synthetic JS Distance	0.16765376509292115	0.16608978069498795
% Genome Enriched	39.14627475875066	39.234310308344014
Diff. Enrichment	11.334213701813106	11.254355312847174
CHANCE Divergence	0.0964896168935321	0.09580217638416358

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	0.498101139586024	0.4135702343858975	0.3721769339039146	0.38790539818006836	0.3876100324881802	0.37570694419337347	0.4766078172365936	0.4989502521329983	0.4660225727069796

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	0.2976925526754876	0.1871736277460232	0.1788097915367488	0.3180152012271807

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	0.032477309563278045	0.023889257482270797	0.02126524483115635	0.03349350980988609

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