QC Report

	general
Report generated at	2021-09-01 03:46:19
Title	T26A8.4_OP692_L4larva_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	22560252	22863874	23317656
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	22166301	22383894	23220165
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	98.3	97.89999999999999	99.6
Paired Reads	22560252	22863874	23317656
Paired Reads (QC-failed)	0	0	0
Read1	11280126	11431937	11658828
Read1 (QC-failed)	0	0	0
Read2	11280126	11431937	11658828
Read2 (QC-failed)	0	0	0
Properly Paired Reads	22038962	22253062	22983248
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	97.7	97.3	98.6
With itself	22149440	22365876	23204274
With itself (QC-failed)	0	0	0
Singletons	16861	18018	15891
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	6226	6574	91635
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	10144178	10247616	10509143
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1266814	1321888	1201735
Paired Optical Duplicate Reads	86583	89868	92817
% Duplicate Reads	12.488100000000001	12.8995	11.4351

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	17754728	17851456	18614816
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	17754728	17851456	18614816
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	17754728	17851456	18614816
Paired Reads (QC-failed)	0	0	0
Read1	8877364	8925728	9307408
Read1 (QC-failed)	0	0	0
Read2	8877364	8925728	9307408
Read2 (QC-failed)	0	0	0
Properly Paired Reads	17754728	17851456	18614816
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	17754728	17851456	18614816
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	10016550	10077571	10313325
Distinct Fragments	8773982	8793376	9151697
Positions with Two Read	998965	1026575	963553
NRF = Distinct/Total	0.875949	0.872569	0.887366
PBC1 = OneRead/Distinct	0.873044	0.869455	0.884457
PBC2 = OneRead/TwoRead	7.668008	7.447526	8.40045

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	51174	2810
N1	49336	1933
N2	46244	2141
Np	52376	2993
N optimal	52376	2993
N conservative	51174	2810
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0234884902489545	1.0651245551601423
Self Consistency Ratio	1.0668627281377043	1.107604759441283
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	81252	76348

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	90.0	94.0	105.0	105.0
25 percentile	360.0	376.0	359.0	420.0
50 percentile (median)	360.0	376.0	420.0	420.0
75 percentile	360.0	376.0	420.0	420.0
Max size	1695.0	4300.0	4344.0	4344.0
Mean	359.30543248166197	375.70842720176034	448.3050451052456	421.198506949748

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	9499995	9572187
Estimated Fragment Length	160	155
Cross-correlation at Estimated Fragment Length	0.749948280434162	0.750718327027602
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.748417	0.7494876
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7404265	0.7396175
NSC (Normalized Strand Cross-correlation coeff.)	1.01286	1.015009
RSC (Relative Strand Cross-correlation coeff.)	1.191636	1.124697

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	0.38796903504157537	0.3806722355230738
Synthetic AUC	0.49848886334075126	0.4984817985044471
X-intercept	0.01851012375362704	0.018805678647956178
Synthetic X-intercept	0.0	0.0
Elbow Point	0.6053123995263133	0.6358284423657972
Synthetic Elbow Point	0.4998484406309055	0.5020081296223398
JS Distance	0.08351704275310712	0.09564370609565942
Synthetic JS Distance	0.18033998659133013	0.19491946038619262
% Genome Enriched	37.52448812088994	33.57863058234299
Diff. Enrichment	11.816521025399057	12.38729730350272
CHANCE Divergence	0.10074670476621582	0.10637883277979829

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	0.4170300440536177	0.4002298748068505	0.44661343164479905	0.4316124130154986	0.44798512261072093	0.42907839002039944	0.384115467133462	0.40758026751757503	0.40714747752806085

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	0.309655704750613	0.29656675112116615	0.2895873031309043	0.3154117835261425

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	0.041296730927414184	0.028878617571612475	0.034774194329022796	0.04334435276748556

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