QC Report

	general
Report generated at	2021-08-28 09:47:19
Title	C17E4.6_RW12293_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	12911468	11556810	14857176
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	12884193	11535136	14834861
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.8	99.8	99.8
Paired Reads	12911468	11556810	14857176
Paired Reads (QC-failed)	0	0	0
Read1	6455734	5778405	7428588
Read1 (QC-failed)	0	0	0
Read2	6455734	5778405	7428588
Read2 (QC-failed)	0	0	0
Properly Paired Reads	12840360	11488544	14759740
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.4	99.4	99.3
With itself	12877040	11528986	14828312
With itself (QC-failed)	0	0	0
Singletons	7153	6150	6549
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.0
Diff. Chroms	5767	4959	19613
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	5862690	5207604	6758877
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	995157	790919	1122172
Paired Optical Duplicate Reads	48933	38987	56917
% Duplicate Reads	16.9744	15.187800000000001	16.6029

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	9735066	8833370	11273410
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	9735066	8833370	11273410
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	9735066	8833370	11273410
Paired Reads (QC-failed)	0	0	0
Read1	4867533	4416685	5636705
Read1 (QC-failed)	0	0	0
Read2	4867533	4416685	5636705
Read2 (QC-failed)	0	0	0
Properly Paired Reads	9735066	8833370	11273410
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	9735066	8833370	11273410
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	5832693	5177911	6691695
Distinct Fragments	4844831	4392669	5582796
Positions with Two Read	731193	603114	834631
NRF = Distinct/Total	0.830634	0.848348	0.834287
PBC1 = OneRead/Distinct	0.824451	0.843301	0.827591
PBC2 = OneRead/TwoRead	5.462755	6.142026	5.535704

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	42747	955
N1	31253	570
N2	33233	414
Np	44380	1017
N optimal	44380	1017
N conservative	42747	955
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0382015112171614	1.0649214659685864
Self Consistency Ratio	1.0633539180238698	1.3768115942028984
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	81034	86576

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	61.0	71.0	71.0
25 percentile	280.0	244.0	284.0	284.0
50 percentile (median)	280.0	244.0	284.0	284.0
75 percentile	280.0	244.0	284.0	284.0
Max size	280.0	244.0	284.0	284.0
Mean	279.94634351013156	243.97113518758084	276.795476892822	283.8312978819288

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	5497310	4880598
Estimated Fragment Length	185	140
Cross-correlation at Estimated Fragment Length	0.611113159846889	0.590339327781456
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6110863	0.5904645
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6064922	0.5860346
NSC (Normalized Strand Cross-correlation coeff.)	1.007619	1.007345
RSC (Relative Strand Cross-correlation coeff.)	1.005856	0.971751

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	0.4013524917103809	0.400263567172178
Synthetic AUC	0.49795710252628855	0.4978482881869569
X-intercept	0.019549493449572485	0.019906753207354362
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5350354066374472	0.5280379054598872
Synthetic Elbow Point	0.5000499842070442	0.503048241037697
JS Distance	0.05400416500767803	0.05227296806800567
Synthetic JS Distance	0.1454525023735886	0.1465055710023451
% Genome Enriched	42.1073535634166	43.8940515252397
Diff. Enrichment	10.263203071179989	10.372537568091989
CHANCE Divergence	0.08724527690652016	0.08825937147040916

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	0.39736238049130845	0.3939126290419172	0.40601421582263214	0.4216713617404543	0.39706693248241615	0.42141479897588324	0.5261040832948989	0.4054761735503898	0.40114598798649237

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	0.21854064607272256	0.17501514627635806	0.16949793793308782	0.22548549592437403

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	0.010828214072526087	0.007696712071597666	0.005363864527354792	0.011359868973348106

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