QC Report

	general
Report generated at	2021-09-01 13:58:06
Title	Y95B8A.8_RW12277_youngadult_1_3
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	14300710	14009676	15102748
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14252578	13959408	15074322
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.7	99.6	99.8
Paired Reads	14300710	14009676	15102748
Paired Reads (QC-failed)	0	0	0
Read1	7150355	7004838	7551374
Read1 (QC-failed)	0	0	0
Read2	7150355	7004838	7551374
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14206652	13913544	14964202
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.3	99.3	99.1
With itself	14241508	13947264	15062804
With itself (QC-failed)	0	0	0
Singletons	11070	12144	11518
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	5420	5268	11643
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	6486144	6348128	6829811
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1121484	1020684	1062845
Paired Optical Duplicate Reads	66714	60808	67867
% Duplicate Reads	17.2905	16.078500000000002	15.561900000000001

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	10729320	10654888	11533932
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	10729320	10654888	11533932
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	10729320	10654888	11533932
Paired Reads (QC-failed)	0	0	0
Read1	5364660	5327444	5766966
Read1 (QC-failed)	0	0	0
Read2	5364660	5327444	5766966
Read2 (QC-failed)	0	0	0
Properly Paired Reads	10729320	10654888	11533932
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	10729320	10654888	11533932
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	6452106	6314853	6769171
Distinct Fragments	5342578	5306035	5721680
Positions with Two Read	808397	751887	794234
NRF = Distinct/Total	0.828036	0.840247	0.845256
PBC1 = OneRead/Distinct	0.822513	0.835726	0.840453
PBC2 = OneRead/TwoRead	5.435869	5.89768	6.054645

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	62467	1538
N1	29969	733
N2	31615	667
Np	70180	1694
N optimal	70180	1694
N conservative	62467	1538
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.123473193846351	1.1014304291287387
Self Consistency Ratio	1.0549234208682305	1.0989505247376312
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	119262	98710

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	68.0	64.0	72.0	72.0
25 percentile	270.0	256.0	290.0	290.0
50 percentile (median)	270.0	256.0	290.0	290.0
75 percentile	270.0	256.0	290.0	290.0
Max size	289.0	330.0	763.0	763.0
Mean	269.94503697741106	255.94519298956538	281.3099173553719	289.7943858649188

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	6063638	5927678
Estimated Fragment Length	170	150
Cross-correlation at Estimated Fragment Length	0.633249536836194	0.632986557060746
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6331945	0.6330394
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6282045	0.6280359
NSC (Normalized Strand Cross-correlation coeff.)	1.008031	1.007883
RSC (Relative Strand Cross-correlation coeff.)	1.011025	0.9894394

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	0.39865019518891515	0.40148810723381595
Synthetic AUC	0.4980512084949415	0.49804323776456794
X-intercept	0.019505350848831034	0.019553251024864184
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5514048722462388	0.5437228815149229
Synthetic Elbow Point	0.5004854649850741	0.49991280056547815
JS Distance	0.0603327973514023	0.054988620817876116
Synthetic JS Distance	0.15133310788280044	0.14686501115669362
% Genome Enriched	40.258301699258745	41.61826753046651
Diff. Enrichment	10.58798192890582	10.190398229478198
CHANCE Divergence	0.09005417695005236	0.08662648756292722

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	0.5147578784116794	0.4391804024594158	0.37637557645778114	0.3772625296483642	0.3760508587683096	0.3968400230955032	0.5060493238748893	0.5025850852180264	0.5045222156462377

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	0.30205084050809833	0.16708337527448153	0.16701808597143394	0.33170164637381006

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	0.01691168548304431	0.009889722741049758	0.008665975653615505	0.01823228618053098

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