QC Report

	general
Report generated at	2021-08-28 17:41:38
Title	D1046.2_OP397_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	21439086	23303312	17796330
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	21378802	23197377	17747464
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.7	99.5	99.7
Paired Reads	21439086	23303312	17796330
Paired Reads (QC-failed)	0	0	0
Read1	10719543	11651656	8898165
Read1 (QC-failed)	0	0	0
Read2	10719543	11651656	8898165
Read2 (QC-failed)	0	0	0
Properly Paired Reads	21295862	23109914	17667058
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.3	99.2	99.3
With itself	21355776	23170486	17726482
With itself (QC-failed)	0	0	0
Singletons	23026	26891	20982
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	8637	8454	16359
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	9790093	10615561	8145902
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1885632	2207127	1473639
Paired Optical Duplicate Reads	198010	228007	172777
% Duplicate Reads	19.2606	20.7914	18.090600000000002

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	15808922	16816868	13344526
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	15808922	16816868	13344526
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	15808922	16816868	13344526
Paired Reads (QC-failed)	0	0	0
Read1	7904461	8408434	6672263
Read1 (QC-failed)	0	0	0
Read2	7904461	8408434	6672263
Read2 (QC-failed)	0	0	0
Properly Paired Reads	15808922	16816868	13344526
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	15808922	16816868	13344526
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	9736732	10548764	8040213
Distinct Fragments	7880478	8378536	6602698
Positions with Two Read	1309071	1502839	1054831
NRF = Distinct/Total	0.809356	0.794267	0.821209
PBC1 = OneRead/Distinct	0.801947	0.784112	0.813233
PBC2 = OneRead/TwoRead	4.827644	4.371533	5.090419

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	82888	1546
N1	68505	619
N2	69055	463
Np	83773	1641
N optimal	83773	1641
N conservative	82888	1546
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0106770581990154	1.0614489003880982
Self Consistency Ratio	1.0080286110502883	1.3369330453563715
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	121345	131687

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	71.0	69.0	74.0	74.0
25 percentile	284.0	276.0	296.0	296.0
50 percentile (median)	284.0	276.0	296.0	296.0
75 percentile	284.0	276.0	296.0	296.0
Max size	370.0	335.0	394.0	394.0
Mean	283.94756273435246	275.9584772984425	290.91285801340644	295.9003497546942

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	9188412	9956719
Estimated Fragment Length	185	155
Cross-correlation at Estimated Fragment Length	0.716558325198201	0.726647403959759
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7160268	0.7264103
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7115567	0.7224403
NSC (Normalized Strand Cross-correlation coeff.)	1.007029	1.005823
RSC (Relative Strand Cross-correlation coeff.)	1.118917	1.059729

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	0.41472197807321565	0.42065748205976466
Synthetic AUC	0.49840130983559083	0.4984485096991143
X-intercept	0.018662274133972246	0.018528501547369472
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5151662174303684	0.5055545572526705
Synthetic Elbow Point	0.5013484704091695	0.49884795595843495
JS Distance	0.04387733319424195	0.035056950482170245
Synthetic JS Distance	0.13081732249289557	0.12491636025947343
% Genome Enriched	44.386542877108916	43.648198063292405
Diff. Enrichment	9.15947831596235	8.11281791694145
CHANCE Divergence	0.0778699857957095	0.06894186523723739

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	0.5189358894932874	0.5403804085279138	0.5343015122344823	0.5150858055138448	0.5342554709619632	0.5456835363160369	0.5152548643266569	0.5313111785914653	0.5263512409263494

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	0.37352021207762326	0.32398502567094706	0.31316758863778915	0.37720937945104166

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	0.013369178186949649	0.007451488469612286	0.005301879041923859	0.014000090112760488

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