QC Report

	general
Report generated at	2021-08-30 12:41:34
Title	F33H1.4_RW12303_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}, 'ctl2': {'paired_end': True}}
Peak caller	spp

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1	ctl2
Total Reads	21551592	18995012	20795578	16447800
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	21480894	18938547	20730933	16409571
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	99.7	99.7	99.7	99.8
Paired Reads	21551592	18995012	20795578	16447800
Paired Reads (QC-failed)	0	0	0	0
Read1	10775796	9497506	10397789	8223900
Read1 (QC-failed)	0	0	0	0
Read2	10775796	9497506	10397789	8223900
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	21376298	18870170	20610764	16345026
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	99.2	99.3	99.1	99.4
With itself	21459960	18923482	20705072	16395710
With itself (QC-failed)	0	0	0	0
Singletons	20934	15065	25861	13861
Singletons (QC-failed)	0	0	0	0
% Singleton	0.1	0.1	0.1	0.1
Diff. Chroms	7564	6134	39102	11324
Diff. Chroms (QC-failed)	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2
Unpaired Reads	0	0	0	0
Paired Reads	9795039	8684412	9459804	7507946
Unmapped Reads	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0
Paired Duplicate Reads	1741330	1284032	1493279	913909
Paired Optical Duplicate Reads	159730	121851	141255	106867
% Duplicate Reads	17.7777	14.785499999999999	15.785499999999999	12.1726

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	ctl2
Total Reads	16107418	14800760	15933050	13188074
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	16107418	14800760	15933050	13188074
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0
Paired Reads	16107418	14800760	15933050	13188074
Paired Reads (QC-failed)	0	0	0	0
Read1	8053709	7400380	7966525	6594037
Read1 (QC-failed)	0	0	0	0
Read2	8053709	7400380	7966525	6594037
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	16107418	14800760	15933050	13188074
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	100.0	100.0	100.0	100.0
With itself	16107418	14800760	15933050	13188074
With itself (QC-failed)	0	0	0	0
Singletons	0	0	0	0
Singletons (QC-failed)	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0
Diff. Chroms (QC-failed)	0	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	ctl2
Total Fragments	9740837	8643393	9369623	7434022
Distinct Fragments	8017538	7371588	7900285	6534148
Positions with Two Read	1247448	989329	1103313	742304
NRF = Distinct/Total	0.823085	0.852858	0.843181	0.878952
PBC1 = OneRead/Distinct	0.817007	0.847763	0.838709	0.874892
PBC2 = OneRead/TwoRead	5.251028	6.316763	6.005589	7.701261

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	31497	3165
N1	23552	2219
N2	21667	2733
Np	31009	3250
N optimal	31497	3250
N conservative	31497	3165
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0157373665709954	1.0268562401263823
Self Consistency Ratio	1.086998661559053	1.231635872014421
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	67615	58604

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	85.0	85.0	85.0
25 percentile	310.0	340.0	238.0	340.0
50 percentile (median)	310.0	340.0	340.0	340.0
75 percentile	310.0	340.0	340.0	340.0
Max size	771.0	909.0	933.0	933.0
Mean	308.52100865192637	338.01527199508564	300.9913846153846	335.7991237260691

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	9170147	8107005
Estimated Fragment Length	155	165
Cross-correlation at Estimated Fragment Length	0.724277268368307	0.713007108430159
Phantom Peak	55	55
Cross-correlation at Phantom Peak	0.7149897	0.6959266
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7021627	0.6757287
NSC (Normalized Strand Cross-correlation coeff.)	1.031495	1.055168
RSC (Relative Strand Cross-correlation coeff.)	1.724062	1.845657

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	0.3955609215900333	0.3833856379536129
Synthetic AUC	0.4984093244193228	0.49834402557357244
X-intercept	0.01942348385036132	0.01939154389747275
Synthetic X-intercept	0.0	0.0
Elbow Point	0.598486844731904	0.638248093584062
Synthetic Elbow Point	0.5002320826023485	0.5019624596770786
JS Distance	0.10448174059081353	0.13786657671355673
Synthetic JS Distance	0.17308752927514054	0.19933580619647062
% Genome Enriched	34.442248572683354	30.09082924102687
Diff. Enrichment	10.508067278762745	12.246396003334503
CHANCE Divergence	0.09031797077714677	0.10679047467004008

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	0.3674289076002125	0.3665189490269419	0.3475704985652575	0.35750839821738883	0.3418544600822379	0.3631858093773563	0.4429533504045434	0.37923274680036156	0.3501717474366653

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	0.22053917251285404	0.16926375164535992	0.19107660687694417	0.21850003581576372

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	0.0679763459366644	0.04846183292691603	0.07644729054453961	0.06877335182940904

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