QC Report

	general
Report generated at	2021-08-28 11:03:09
Title	bed-1_RW12201_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	17973996	20670876	18350580
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	17801184	20260395	18178653
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.0	98.0	99.1
Paired Reads	17973996	20670876	18350580
Paired Reads (QC-failed)	0	0	0
Read1	8986998	10335438	9175290
Read1 (QC-failed)	0	0	0
Read2	8986998	10335438	9175290
Read2 (QC-failed)	0	0	0
Properly Paired Reads	17747862	20202010	18106896
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.7	97.7	98.7
With itself	17792206	20248570	18168866
With itself (QC-failed)	0	0	0
Singletons	8978	11825	9787
Singletons (QC-failed)	0	0	0
% Singleton	0.0	0.1	0.1
Diff. Chroms	6796	5754	17056
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	8073094	9215762	8292540
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1215647	1403264	1049900
Paired Optical Duplicate Reads	118678	132184	109635
% Duplicate Reads	15.058	15.226799999999999	12.6608

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	13714894	15624996	14485280
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	13714894	15624996	14485280
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	13714894	15624996	14485280
Paired Reads (QC-failed)	0	0	0
Read1	6857447	7812498	7242640
Read1 (QC-failed)	0	0	0
Read2	6857447	7812498	7242640
Read2 (QC-failed)	0	0	0
Properly Paired Reads	13714894	15624996	14485280
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	13714894	15624996	14485280
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	8003992	9143236	8189037
Distinct Fragments	6803625	7758417	7158047
Positions with Two Read	930704	1065120	839758
NRF = Distinct/Total	0.850029	0.848542	0.874101
PBC1 = OneRead/Distinct	0.844589	0.843407	0.869977
PBC2 = OneRead/TwoRead	6.174109	6.143445	7.41563

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	91913	523
N1	37993	91
N2	41680	99
Np	91272	589
N optimal	91913	589
N conservative	91913	523
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.007022964326409	1.1261950286806883
Self Consistency Ratio	1.0970441923512226	1.0879120879120878
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	144952	148047

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	70.0	104.0	88.0	88.0
25 percentile	244.0	240.0	260.0	260.0
50 percentile (median)	244.0	240.0	260.0	260.0
75 percentile	244.0	240.0	260.0	260.0
Max size	244.0	240.0	260.0	260.0
Mean	243.99621943815885	239.9971495538579	258.4855687606112	259.9902951704329

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7534002	8604632
Estimated Fragment Length	145	150
Cross-correlation at Estimated Fragment Length	0.690761451728475	0.718883006466912
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6905366	0.7188851
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.686818	0.7148214
NSC (Normalized Strand Cross-correlation coeff.)	1.005742	1.005682
RSC (Relative Strand Cross-correlation coeff.)	1.060455	0.999484

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	0.4164627456761732	0.418349709718022
Synthetic AUC	0.4982758117030838	0.4983821177379419
X-intercept	0.019175949215474906	0.019261787838862936
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5007585738811036	0.4971293967341398
Synthetic Elbow Point	0.49955407688502035	0.5023640223535035
JS Distance	0.02996088409440489	0.029748023851879964
Synthetic JS Distance	0.13064361527359608	0.12770054861708707
% Genome Enriched	45.84481175390266	44.32267337405678
Diff. Enrichment	7.827719868937627	7.5506185001343376
CHANCE Divergence	0.06664493528601821	0.06418471490626813

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	0.5583004870471474	0.5575903507431298	0.40896103040081383	0.4080230164538922	0.40646123935937667	0.4083422485356156	0.5544510221408465	0.5575190937989819	0.5563377747045252

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	0.3715390548498989	0.1727532126752128	0.18332503893120997	0.3694321962352279

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	0.004050833183082827	0.0010447765764722643	0.0010631042721546936	0.004423465800314862

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