QC Report

	general
Report generated at	2021-09-01 07:54:39
Title	Y105C5A.15_OP773_L4larva_2_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	10844498	11246978	10227384
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	10697873	11168101	10166939
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	98.6	99.3	99.4
Paired Reads	10844498	11246978	10227384
Paired Reads (QC-failed)	0	0	0
Read1	5422249	5623489	5113692
Read1 (QC-failed)	0	0	0
Read2	5422249	5623489	5113692
Read2 (QC-failed)	0	0	0
Properly Paired Reads	10613902	11110142	10097146
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	97.89999999999999	98.8	98.7
With itself	10687552	11160036	10157258
With itself (QC-failed)	0	0	0
Singletons	10321	8065	9681
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	3278	3349	31503
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	4855685	5083216	4649886
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	723471	610830	508051
Paired Optical Duplicate Reads	31160	25386	23073
% Duplicate Reads	14.8995	12.0166	10.9261

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	8264428	8944772	8283670
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	8264428	8944772	8283670
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	8264428	8944772	8283670
Paired Reads (QC-failed)	0	0	0
Read1	4132214	4472386	4141835
Read1 (QC-failed)	0	0	0
Read2	4132214	4472386	4141835
Read2 (QC-failed)	0	0	0
Properly Paired Reads	8264428	8944772	8283670
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	8264428	8944772	8283670
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	4784256	5015014	4576643
Distinct Fragments	4077129	4416272	4079148
Positions with Two Read	546033	484556	410802
NRF = Distinct/Total	0.852197	0.88061	0.891297
PBC1 = OneRead/Distinct	0.847518	0.878068	0.889172
PBC2 = OneRead/TwoRead	6.32826	8.002759	8.829229

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	62420	848
N1	34159	350
N2	35787	329
Np	74864	1046
N optimal	74864	1046
N conservative	62420	848
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.19935917975008	1.2334905660377358
Self Consistency Ratio	1.0476594748089816	1.0638297872340425
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	98627	132573

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	58.0	77.0	64.0	64.0
25 percentile	230.0	240.0	256.0	256.0
50 percentile (median)	230.0	240.0	256.0	256.0
75 percentile	230.0	240.0	256.0	256.0
Max size	230.0	240.0	256.0	256.0
Mean	229.99496081194803	239.99877048871187	254.03632887189292	255.97256358196196

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	4517944	4724637
Estimated Fragment Length	120	130
Cross-correlation at Estimated Fragment Length	0.576037222041834	0.59908318882553
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.5765734	0.5997867
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.5711996	0.5947514
NSC (Normalized Strand Cross-correlation coeff.)	1.008469	1.007283
RSC (Relative Strand Cross-correlation coeff.)	0.9002226	0.8602913

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	0.3947002876478355	0.3981928814080927
Synthetic AUC	0.4977557412149448	0.4978502127176802
X-intercept	0.01972221667897268	0.01954061982399074
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5459080840534014	0.5413202690028137
Synthetic Elbow Point	0.49948298361256316	0.49885747707680694
JS Distance	0.04287509898028698	0.03899205396284902
Synthetic JS Distance	0.16455001514756928	0.15934930533532532
% Genome Enriched	43.259164654467085	42.82133663267546
Diff. Enrichment	11.206499981951252	10.750369295205592
CHANCE Divergence	0.09533685849842674	0.09141291888876747

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	0.41246145528764966	0.5224474139754485	0.4050187139388231	0.4115514626868074	0.4105765093482574	0.4098677976364294	0.5152765381307672	0.5061031308834809	0.5144867861376473

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	0.27060235223020246	0.16373958367112643	0.17198649669326396	0.31465030332612787

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	0.00855751574739093	0.004379734447441492	0.004088980691738146	0.01010587360249169

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