QC Report

	general
Report generated at	2021-08-31 01:12:02
Title	mcd-1_RW12215_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	17019898	16701990	18484228
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	16766557	13645856	18388681
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	98.5	81.69999999999999	99.5
Paired Reads	17019898	16701990	18484228
Paired Reads (QC-failed)	0	0	0
Read1	8509949	8350995	9242114
Read1 (QC-failed)	0	0	0
Read2	8509949	8350995	9242114
Read2 (QC-failed)	0	0	0
Properly Paired Reads	16664920	13422842	18259092
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	97.89999999999999	80.4	98.8
With itself	16755532	13606620	18369684
With itself (QC-failed)	0	0	0
Singletons	11025	39236	18997
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.2	0.1
Diff. Chroms	6175	26926	51465
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	7691592	6082855	8427409
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	985023	1929642	651164
Paired Optical Duplicate Reads	32114	28026	34755
% Duplicate Reads	12.806500000000002	31.7226	7.7267

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	13413138	8306426	15552490
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	13413138	8306426	15552490
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	13413138	8306426	15552490
Paired Reads (QC-failed)	0	0	0
Read1	6706569	4153213	7776245
Read1 (QC-failed)	0	0	0
Read2	6706569	4153213	7776245
Read2 (QC-failed)	0	0	0
Properly Paired Reads	13413138	8306426	15552490
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	13413138	8306426	15552490
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	7634582	6015902	8335219
Distinct Fragments	6659693	4120716	7695831
Positions with Two Read	768112	967083	558967
NRF = Distinct/Total	0.872306	0.684971	0.923291
PBC1 = OneRead/Distinct	0.870054	0.669433	0.922351
PBC2 = OneRead/TwoRead	7.543554	2.852436	12.698889

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	40898	3903
N1	29499	3339
N2	30526	3051
Np	42891	4460
N optimal	42891	4460
N conservative	40898	3903
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.04873098929043	1.142710735331796
Self Consistency Ratio	1.0348147394826943	1.0943952802359882
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	75583	65169

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	90.0	86.0	92.0	92.0
25 percentile	360.0	344.0	278.75	370.0
50 percentile (median)	360.0	344.0	370.0	370.0
75 percentile	360.0	344.0	370.0	370.0
Max size	714.0	666.0	1082.0	1082.0
Mean	358.01430215789264	341.597277846829	327.5038116591928	365.45230934228624

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7203596	5657934
Estimated Fragment Length	185	185
Cross-correlation at Estimated Fragment Length	0.700251145151816	0.599637732185946
Phantom Peak	55	55
Cross-correlation at Phantom Peak	0.6819547	0.5716799
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6658467	0.5544123
NSC (Normalized Strand Cross-correlation coeff.)	1.05167	1.081574
RSC (Relative Strand Cross-correlation coeff.)	2.135857	2.619093

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	0.3588118710808546	0.3315197260673096
Synthetic AUC	0.4982633087948474	0.4977730576496217
X-intercept	0.019198297919901644	0.019892861562289185
Synthetic X-intercept	0.0	0.0
Elbow Point	0.6389426665655424	0.6506304961339949
Synthetic Elbow Point	0.5030420231954128	0.500214608325222
JS Distance	0.14332728703261033	0.17614363317365464
Synthetic JS Distance	0.2246555260609486	0.25933996891547745
% Genome Enriched	28.432202205838326	30.40252757297908
Diff. Enrichment	14.292476319050563	18.702691880034617
CHANCE Divergence	0.12423253458707693	0.16049593002586718

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	0.44484959447968103	0.440722038575917	0.4069284298829357	0.45251942230763936	0.405653830692539	0.4488670455541398	0.40983124707291546	0.4410305030007963	0.4390728909793753

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	0.30849339332962666	0.2509046727171524	0.28551136192629656	0.3185700689019356

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	0.08963342910566713	0.08101251176272099	0.09062862896750058	0.09551158577584706

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