QC Report

	general
Report generated at	2021-08-31 14:20:33
Title	nfyb-1_RW12190_youngadult_1_5
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	24044040	27061590	14762500
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	23898541	26948838	14716916
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.4	99.6	99.7
Paired Reads	24044040	27061590	14762500
Paired Reads (QC-failed)	0	0	0
Read1	12022020	13530795	7381250
Read1 (QC-failed)	0	0	0
Read2	12022020	13530795	7381250
Read2 (QC-failed)	0	0	0
Properly Paired Reads	23850490	26899222	14662608
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.2	99.4	99.3
With itself	23887980	26935028	14709518
With itself (QC-failed)	0	0	0
Singletons	10561	13810	7398
Singletons (QC-failed)	0	0	0
% Singleton	0.0	0.1	0.1
Diff. Chroms	4531	5333	20389
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	10948142	12344375	6759215
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1283915	1465079	617517
Paired Optical Duplicate Reads	70403	81795	40527
% Duplicate Reads	11.7272	11.8684	9.1359

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	19328454	21758592	12283396
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	19328454	21758592	12283396
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	19328454	21758592	12283396
Paired Reads (QC-failed)	0	0	0
Read1	9664227	10879296	6141698
Read1 (QC-failed)	0	0	0
Read2	9664227	10879296	6141698
Read2 (QC-failed)	0	0	0
Properly Paired Reads	19328454	21758592	12283396
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	19328454	21758592	12283396
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	10782533	12161408	6661692
Distinct Fragments	9530345	10733787	6057415
Positions with Two Read	1021784	1165066	522142
NRF = Distinct/Total	0.883869	0.882611	0.909291
PBC1 = OneRead/Distinct	0.881343	0.879888	0.907296
PBC2 = OneRead/TwoRead	8.220426	8.106438	10.525623

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	68009	3890
N1	34962	1734
N2	54986	2433
Np	68369	4061
N optimal	68369	4061
N conservative	68009	3890
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0052934170477437	1.0439588688946015
Self Consistency Ratio	1.5727361134946514	1.4031141868512111
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	103248	97308

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	82.0	88.0	94.0	94.0
25 percentile	330.0	350.0	376.0	376.0
50 percentile (median)	330.0	350.0	376.0	376.0
75 percentile	330.0	350.0	376.0	376.0
Max size	739.0	1349.0	1378.0	1378.0
Mean	329.6573783511545	349.56836025814937	361.21644915045556	375.0804019365502

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	10171285	11467870
Estimated Fragment Length	165	160
Cross-correlation at Estimated Fragment Length	0.764547518907879	0.784340271434184
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.763578	0.7828629
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7568165	0.7759596
NSC (Normalized Strand Cross-correlation coeff.)	1.010215	1.0108
RSC (Relative Strand Cross-correlation coeff.)	1.14339	1.214008

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	0.3951607224262409	0.39286584619579323
Synthetic AUC	0.4985448693929947	0.49863025336902583
X-intercept	0.018927155015755988	0.018677535435995544
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5793271054912313	0.5807429477476326
Synthetic Elbow Point	0.5013454345456839	0.49970659192431066
JS Distance	0.06463867717454731	0.06843519323993548
Synthetic JS Distance	0.17059451763041825	0.1737968644966066
% Genome Enriched	36.0792152759195	35.00125808268199
Diff. Enrichment	9.868607842783328	10.065454199750889
CHANCE Divergence	0.08434595601024017	0.08621331021687834

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	0.48180532183277563	0.470682891613575	0.35810930785159456	0.43169907317532313	0.371913074052697	0.49612180788168647	0.45747545345557333	0.47551505768922603	0.47682018691828987

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	0.3681999187773197	0.21750027187896145	0.31674793111613103	0.37094170751530786

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	0.04893160243255259	0.028833294168276468	0.03598992067133756	0.05086593472794321

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