QC Report

	general
Report generated at	2021-08-31 01:36:58
Title	mec-3_OP55_lateembryonic_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	20423656	19512136	20687354
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	20363452	19455715	20633291
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.7	99.7	99.7
Paired Reads	20423656	19512136	20687354
Paired Reads (QC-failed)	0	0	0
Read1	10211828	9756068	10343677
Read1 (QC-failed)	0	0	0
Read2	10211828	9756068	10343677
Read2 (QC-failed)	0	0	0
Properly Paired Reads	20239018	19327614	20305380
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.1	99.1	98.2
With itself	20334136	19426642	20592402
With itself (QC-failed)	0	0	0
Singletons	29316	29073	40889
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.2
Diff. Chroms	14340	11515	12911
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	8968752	8554451	9293918
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1686511	1481899	1624187
Paired Optical Duplicate Reads	184177	153047	210194
% Duplicate Reads	18.804299999999998	17.3231	17.4758

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	14564482	14145104	15339462
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14564482	14145104	15339462
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	14564482	14145104	15339462
Paired Reads (QC-failed)	0	0	0
Read1	7282241	7072552	7669731
Read1 (QC-failed)	0	0	0
Read2	7282241	7072552	7669731
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14564482	14145104	15339462
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	14564482	14145104	15339462
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	8937350	8524920	9253267
Distinct Fragments	7272461	7063874	7654441
Positions with Two Read	1196763	1070544	1185535
NRF = Distinct/Total	0.813716	0.828615	0.827215
PBC1 = OneRead/Distinct	0.805759	0.822902	0.81995
PBC2 = OneRead/TwoRead	4.89642	5.429837	5.294033

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	79502	745
N1	34574	333
N2	36235	350
Np	80111	843
N optimal	80111	843
N conservative	79502	745
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0076601846494428	1.131543624161074
Self Consistency Ratio	1.0480418811823915	1.0510510510510511
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	129444	126248

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	80.0	75.0	79.0	79.0
25 percentile	296.0	300.0	316.0	316.0
50 percentile (median)	296.0	300.0	316.0	316.0
75 percentile	296.0	300.0	316.0	316.0
Max size	296.0	300.0	316.0	316.0
Mean	295.9664951639319	299.960728090742	306.7437722419929	315.9019360637116

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	8424299	8036715
Estimated Fragment Length	170	200
Cross-correlation at Estimated Fragment Length	0.699188564685106	0.695554758798783
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6999212	0.6962347
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6959035	0.6921709
NSC (Normalized Strand Cross-correlation coeff.)	1.004721	1.004889
RSC (Relative Strand Cross-correlation coeff.)	0.817649	0.8326835

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	0.4225755178951325	0.4204579878760783
Synthetic AUC	0.4983289836088325	0.49830420277345855
X-intercept	0.018345217467681276	0.01857278599774827
Synthetic X-intercept	0.0	0.0
Elbow Point	0.4964866612901938	0.5004112203262614
Synthetic Elbow Point	0.5011917855554601	0.5009980430458559
JS Distance	0.022847771128457147	0.025883389257498862
Synthetic JS Distance	0.11688815245402698	0.11892466953482767
% Genome Enriched	44.244312782963505	43.76282568250597
Diff. Enrichment	7.418934745095268	7.699542912234259
CHANCE Divergence	0.06304891228018515	0.0654299895680293

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	0.5489565643323258	0.5400820665581533	0.3972516980347536	0.4027472685955508	0.39215433712703784	0.40134324922602194	0.5322953455337183	0.5460681637089324	0.5426578803789006

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	0.365359256660824	0.17804416250437194	0.18796107826425312	0.3680617686371374

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	0.007073003421226624	0.0038465494344392063	0.00408975430650775	0.007691681795759786

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