QC Report

	general
Report generated at	2021-08-31 12:43:26
Title	nhr-120_OP415_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	19257824	19031348	20140268
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	19181984	18927894	20074444
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.6	99.5	99.7
Paired Reads	19257824	19031348	20140268
Paired Reads (QC-failed)	0	0	0
Read1	9628912	9515674	10070134
Read1 (QC-failed)	0	0	0
Read2	9628912	9515674	10070134
Read2 (QC-failed)	0	0	0
Properly Paired Reads	19113396	18863698	19976976
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.3	99.1	99.2
With itself	19159960	18907862	20050566
With itself (QC-failed)	0	0	0
Singletons	22024	20032	23878
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	5633	5777	20400
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	8735406	8617450	9156521
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1711623	1576596	1663574
Paired Optical Duplicate Reads	167453	159268	191649
% Duplicate Reads	19.5941	18.2954	18.168200000000002

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	14047566	14081708	14985894
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14047566	14081708	14985894
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	14047566	14081708	14985894
Paired Reads (QC-failed)	0	0	0
Read1	7023783	7040854	7492947
Read1 (QC-failed)	0	0	0
Read2	7023783	7040854	7492947
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14047566	14081708	14985894
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	14047566	14081708	14985894
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	8668839	8553510	9040200
Distinct Fragments	6990654	7005688	7417625
Positions with Two Read	1177872	1120475	1191439
NRF = Distinct/Total	0.806412	0.819042	0.820516
PBC1 = OneRead/Distinct	0.798609	0.811881	0.812295
PBC2 = OneRead/TwoRead	4.739732	5.076227	5.057164

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	86028	555
N1	39658	89
N2	39372	96
Np	86995	610
N optimal	86995	610
N conservative	86028	555
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0112405263402613	1.0990990990990992
Self Consistency Ratio	1.007264045514579	1.0786516853932584
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	140947	137384

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	64.0	64.0	68.0	68.0
25 percentile	256.0	250.0	264.0	264.0
50 percentile (median)	256.0	250.0	264.0	264.0
75 percentile	256.0	250.0	264.0	264.0
Max size	256.0	250.0	264.0	264.0
Mean	255.9959204523686	249.9975543003552	262.6688524590164	263.99045922179437

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	8188824	8067046
Estimated Fragment Length	175	150
Cross-correlation at Estimated Fragment Length	0.690496519518068	0.692926272334725
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6907087	0.6928167
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6869524	0.6890554
NSC (Normalized Strand Cross-correlation coeff.)	1.005159	1.005618
RSC (Relative Strand Cross-correlation coeff.)	0.9435211	1.029123

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	0.41809681010600314	0.41593351500662756
Synthetic AUC	0.4982935251097906	0.4982981064716697
X-intercept	0.01894317446883259	0.01884137237210862
Synthetic X-intercept	0.0	0.0
Elbow Point	0.49799589597821836	0.5062119240197057
Synthetic Elbow Point	0.501316259072611	0.49924401257845874
JS Distance	0.03185714548224185	0.03519991604315969
Synthetic JS Distance	0.12778661627079171	0.129987685796542
% Genome Enriched	45.320696565875934	44.39729166500323
Diff. Enrichment	7.822440009207182	8.247834543339394
CHANCE Divergence	0.0665437563562574	0.07012190219401784

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	0.5546074672295542	0.5434322313742055	0.4175957005511559	0.40747755883022146	0.40383329095350623	0.4115936788349822	0.5443887033842395	0.5525195173882186	0.5473365965532275

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	0.3559872537058724	0.18296998924938312	0.18407383536144906	0.3593889767649176

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	0.004313015686078496	0.0009143932835054842	0.0010576131815828024	0.0046182493014217145

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