QC Report

	general
Report generated at	2021-08-29 12:56:33
Title	egl-18_RW12252_youngadult_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	18748392	15479662	16074196
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	18636240	15363377	16026469
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.4	99.2	99.7
Paired Reads	18748392	15479662	16074196
Paired Reads (QC-failed)	0	0	0
Read1	9374196	7739831	8037098
Read1 (QC-failed)	0	0	0
Read2	9374196	7739831	8037098
Read2 (QC-failed)	0	0	0
Properly Paired Reads	18583734	15321710	15953166
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.1	99.0	99.2
With itself	18627424	15355552	16016534
With itself (QC-failed)	0	0	0
Singletons	8816	7825	9935
Singletons (QC-failed)	0	0	0
% Singleton	0.0	0.1	0.1
Diff. Chroms	3690	3168	23192
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	8494084	7014564	7324688
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1183763	882472	855102
Paired Optical Duplicate Reads	69301	51222	53584
% Duplicate Reads	13.9363	12.5806	11.674199999999999

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	14620642	12264184	12939172
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14620642	12264184	12939172
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	14620642	12264184	12939172
Paired Reads (QC-failed)	0	0	0
Read1	7310321	6132092	6469586
Read1 (QC-failed)	0	0	0
Read2	7310321	6132092	6469586
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14620642	12264184	12939172
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	14620642	12264184	12939172
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	8437663	6956454	7235412
Distinct Fragments	7267145	6085025	6395531
Positions with Two Read	916467	701428	692779
NRF = Distinct/Total	0.861275	0.874731	0.883921
PBC1 = OneRead/Distinct	0.857443	0.871508	0.880726
PBC2 = OneRead/TwoRead	6.799113	7.560507	8.130604

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	80247	597
N1	43405	199
N2	36507	232
Np	88690	699
N optimal	88690	699
N conservative	80247	597
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.105212655924832	1.170854271356784
Self Consistency Ratio	1.1889500643712165	1.1658291457286432
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	143103	118784

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	63.0	66.0	69.0	69.0
25 percentile	250.0	264.0	276.0	276.0
50 percentile (median)	250.0	264.0	276.0	276.0
75 percentile	250.0	264.0	276.0	276.0
Max size	250.0	264.0	276.0	276.0
Mean	249.98864454274195	263.9725804822198	269.19885550786836	275.94632991318076

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7928536	6538069
Estimated Fragment Length	160	160
Cross-correlation at Estimated Fragment Length	0.706297163345223	0.670710868456568
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7065539	0.6708235
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7021734	0.6668345
NSC (Normalized Strand Cross-correlation coeff.)	1.005873	1.005813
RSC (Relative Strand Cross-correlation coeff.)	0.9414009	0.9717527

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	0.4173491320879717	0.4138845887890624
Synthetic AUC	0.4983297759181482	0.49817939198740835
X-intercept	0.019182221122395423	0.019385777776003865
Synthetic X-intercept	0.0	0.0
Elbow Point	0.49659840866592564	0.5067562848116801
Synthetic Elbow Point	0.5004741281214842	0.5025682567131197
JS Distance	0.03424428366146226	0.03335671580395928
Synthetic JS Distance	0.12744401997613716	0.13326536515480303
% Genome Enriched	45.3262793635462	45.15066185847225
Diff. Enrichment	8.067624398229679	8.507629163144708
CHANCE Divergence	0.0686321930497817	0.07238494027641552

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	0.5565981302325849	0.5022634200530586	0.4170244484442683	0.4060144564041114	0.4291171932282034	0.41159313982895235	0.5539698490144589	0.558947894329099	0.5573844188081722

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	0.3466248582006817	0.19747402337051956	0.17894618997888487	0.37715033007838694

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	0.005245821564922905	0.002146417373464175	0.0027857540297829843	0.005911624646557132

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