QC Report

	general
Report generated at	2021-09-01 16:17:42
Title	zip-11_OP761_L4larva_1_3
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	12997900	11130084	11970504
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	12426452	10891198	11908873
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	95.6	97.89999999999999	99.5
Paired Reads	12997900	11130084	11970504
Paired Reads (QC-failed)	0	0	0
Read1	6498950	5565042	5985252
Read1 (QC-failed)	0	0	0
Read2	6498950	5565042	5985252
Read2 (QC-failed)	0	0	0
Properly Paired Reads	12379944	10850194	11754300
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	95.19999999999999	97.5	98.2
With itself	12417670	10883558	11900128
With itself (QC-failed)	0	0	0
Singletons	8782	7640	8745
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	3561	4091	76237
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	5664982	4980323	5346606
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	752176	556254	640318
Paired Optical Duplicate Reads	57199	43926	52454
% Duplicate Reads	13.2776	11.169	11.976199999999999

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	9825612	8848138	9412576
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	9825612	8848138	9412576
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	9825612	8848138	9412576
Paired Reads (QC-failed)	0	0	0
Read1	4912806	4424069	4706288
Read1 (QC-failed)	0	0	0
Read2	4912806	4424069	4706288
Read2 (QC-failed)	0	0	0
Properly Paired Reads	9825612	8848138	9412576
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	9825612	8848138	9412576
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	5590490	4918220	5286394
Distinct Fragments	4852709	4373449	4657390
Positions with Two Read	586237	452327	516466
NRF = Distinct/Total	0.868029	0.889234	0.881015
PBC1 = OneRead/Distinct	0.864454	0.886526	0.877649
PBC2 = OneRead/TwoRead	7.155713	8.57162	7.914471

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	80828	329
N1	33203	155
N2	31707	108
Np	80011	364
N optimal	80828	364
N conservative	80828	329
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0102110959743036	1.1063829787234043
Self Consistency Ratio	1.0471820102816414	1.4351851851851851
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	138063	131194

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	96.0	204.0	70.0	70.0
25 percentile	250.0	280.0	280.0	280.0
50 percentile (median)	250.0	280.0	280.0	280.0
75 percentile	250.0	280.0	280.0	280.0
Max size	265.0	280.0	288.0	288.0
Mean	249.9986310597336	279.9988337881306	278.46153846153845	279.993071707824

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	5257457	4626336
Estimated Fragment Length	140	190
Cross-correlation at Estimated Fragment Length	0.615903555587496	0.592628744494426
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6165279	0.5927921
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6125106	0.5891158
NSC (Normalized Strand Cross-correlation coeff.)	1.005539	1.005963
RSC (Relative Strand Cross-correlation coeff.)	0.8445856	0.9555739

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	0.40818420877620293	0.40997725916624994
Synthetic AUC	0.4979577379138925	0.49785978462067354
X-intercept	0.019268987644861603	0.019237062222647896
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5172576860453979	0.5131832040353733
Synthetic Elbow Point	0.4990989306428185	0.5003943237005422
JS Distance	0.024162018232279828	0.019691206405279625
Synthetic JS Distance	0.14785003171286046	0.14422979704474978
% Genome Enriched	44.03493439325735	44.86838744692398
Diff. Enrichment	9.503626299011458	9.277965846618036
CHANCE Divergence	0.08081187794304658	0.07893407655143948

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	0.5506022423844947	0.5600100269683859	0.3992946190018494	0.41525111492358846	0.40726236696502977	0.41834189709561426	0.5568998192650111	0.557354301374464	0.5562078914206189

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	0.3518976102818127	0.16422915946609737	0.16772161555346446	0.3481750585715242

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	0.010365995046522525	0.009246548713708622	0.007363244108534474	0.01049815918066805

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