QC Report

	general
Report generated at	2021-08-31 21:43:55
Title	sma-4_CS692_L4larva_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	9855968	11392196	10145910
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	9686965	11340008	10116323
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	98.3	99.5	99.7
Paired Reads	9855968	11392196	10145910
Paired Reads (QC-failed)	0	0	0
Read1	4927984	5696098	5072955
Read1 (QC-failed)	0	0	0
Read2	4927984	5696098	5072955
Read2 (QC-failed)	0	0	0
Properly Paired Reads	9651884	11304002	10043278
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	97.89999999999999	99.2	99.0
With itself	9677724	11330890	10106820
With itself (QC-failed)	0	0	0
Singletons	9241	9118	9503
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	2243	2517	11949
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	4442977	5196598	4617380
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	650359	802855	677293
Paired Optical Duplicate Reads	65009	77955	72107
% Duplicate Reads	14.6379	15.4496	14.6683

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	7585236	8787486	7880174
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	7585236	8787486	7880174
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	7585236	8787486	7880174
Paired Reads (QC-failed)	0	0	0
Read1	3792618	4393743	3940087
Read1 (QC-failed)	0	0	0
Read2	3792618	4393743	3940087
Read2 (QC-failed)	0	0	0
Properly Paired Reads	7585236	8787486	7880174
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	7585236	8787486	7880174
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	4401781	5155100	4524441
Distinct Fragments	3761838	4363897	3866158
Positions with Two Read	497806	603406	514871
NRF = Distinct/Total	0.854617	0.84652	0.854505
PBC1 = OneRead/Distinct	0.849995	0.841665	0.849393
PBC2 = OneRead/TwoRead	6.423275	6.087009	6.378077

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	47989	1291
N1	32023	629
N2	36735	641
Np	82569	1606
N optimal	82569	1606
N conservative	47989	1291
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.7205817999958324	1.2439969016266461
Self Consistency Ratio	1.1471442400774443	1.0190779014308426
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	66483	139005

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	62.0	68.0	68.0
25 percentile	250.0	250.0	270.0	270.0
50 percentile (median)	250.0	250.0	270.0	270.0
75 percentile	250.0	250.0	270.0	270.0
Max size	250.0	250.0	302.0	302.0
Mean	249.96430666486168	249.98112298118772	266.35678704856787	269.9302280516901

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	4146675	4857053
Estimated Fragment Length	150	135
Cross-correlation at Estimated Fragment Length	0.55606247290121	0.589792713911814
Phantom Peak	50	55
Cross-correlation at Phantom Peak	0.5563338	0.5899043
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.5508278	0.5854529
NSC (Normalized Strand Cross-correlation coeff.)	1.009503	1.007413
RSC (Relative Strand Cross-correlation coeff.)	0.9507212	0.9749408

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	0.39410971632584213	0.3997247345246206
Synthetic AUC	0.4976802430072759	0.4978460840276792
X-intercept	0.01981954299122856	0.01952822583863424
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5532591605277231	0.5455612045365663
Synthetic Elbow Point	0.5018884641711304	0.5031712413807357
JS Distance	0.059737062061691985	0.05869260441687854
Synthetic JS Distance	0.15979321785447148	0.1516033674747329
% Genome Enriched	43.48327520292435	45.19147119152706
Diff. Enrichment	10.212738971812001	9.573409792006709
CHANCE Divergence	0.08692767202957431	0.08160878005001672

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	0.3224666971469312	0.5611304530101101	0.4275450361729022	0.42573486302342606	0.4273330454055747	0.42369374442104246	0.56182521147064	0.5506796547721686	0.5517783239437308

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	0.2303522896192826	0.1695462079228649	0.18512450546151651	0.35978531853164064

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	0.015095718353979258	0.008886869175856888	0.008593811699956051	0.01785781252500348

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