QC Report

	general
Report generated at	2021-08-30 21:48:51
Title	lin-26_RW12178_youngadult_1_4
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	23861582	30357548	18654210
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	23255902	29516949	18619402
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	97.5	97.2	99.8
Paired Reads	23861582	30357548	18654210
Paired Reads (QC-failed)	0	0	0
Read1	11930791	15178774	9327105
Read1 (QC-failed)	0	0	0
Read2	11930791	15178774	9327105
Read2 (QC-failed)	0	0	0
Properly Paired Reads	23115854	29378182	18378312
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	96.89999999999999	96.8	98.5
With itself	23235042	29484514	18608256
With itself (QC-failed)	0	0	0
Singletons	20860	32435	11146
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	8804	14316	121333
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	10519182	13381219	8364178
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1508826	2090841	828069
Paired Optical Duplicate Reads	104568	133384	61772
% Duplicate Reads	14.3436	15.6252	9.9002

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	18020712	22580756	15072218
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	18020712	22580756	15072218
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	18020712	22580756	15072218
Paired Reads (QC-failed)	0	0	0
Read1	9010356	11290378	7536109
Read1 (QC-failed)	0	0	0
Read2	9010356	11290378	7536109
Read2 (QC-failed)	0	0	0
Properly Paired Reads	18020712	22580756	15072218
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	18020712	22580756	15072218
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	10417144	13230424	8278135
Distinct Fragments	8935264	11185466	7464293
Positions with Two Read	1151711	1544499	690810
NRF = Distinct/Total	0.857746	0.845435	0.901688
PBC1 = OneRead/Distinct	0.853803	0.841133	0.899605
PBC2 = OneRead/TwoRead	6.624022	6.091593	9.720353

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	65939	2655
N1	37338	1193
N2	53628	2098
Np	66842	3201
N optimal	66842	3201
N conservative	65939	2655
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0136944751967727	1.2056497175141243
Self Consistency Ratio	1.4362847501205207	1.7585917854149204
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	111146	95340

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	69.0	80.0	84.0	84.0
25 percentile	276.0	320.0	336.0	336.0
50 percentile (median)	276.0	320.0	336.0	336.0
75 percentile	276.0	320.0	336.0	336.0
Max size	440.0	687.0	683.0	683.0
Mean	275.8118420815864	319.2893643801133	312.05310840362387	334.7939618802549

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	9830359	12449804
Estimated Fragment Length	130	145
Cross-correlation at Estimated Fragment Length	0.747336168246793	0.785535780070446
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7469086	0.7851014
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7410965	0.7781927
NSC (Normalized Strand Cross-correlation coeff.)	1.008419	1.009436
RSC (Relative Strand Cross-correlation coeff.)	1.073574	1.062873

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	0.4019047631281986	0.3982103338097424
Synthetic AUC	0.49848104109764674	0.4986415719823656
X-intercept	0.018672741830176285	0.018451112837110678
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5432306319221623	0.5694487428045452
Synthetic Elbow Point	0.49866146122515614	0.49995750644280146
JS Distance	0.05734702379393753	0.06775447869856169
Synthetic JS Distance	0.15335217675707385	0.16210574584355447
% Genome Enriched	40.34765802047373	37.384019151939654
Diff. Enrichment	9.981950081577711	10.401304819441387
CHANCE Divergence	0.08489825509704516	0.08878229167064706

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	0.4739720051016852	0.44591252834936085	0.37082952105333017	0.473582018245979	0.3714332707830856	0.420500801656065	0.4363312676280572	0.4602219308917599	0.4608956996333236

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	0.33531043754378537	0.19637198574617917	0.2920743663321104	0.3439112595633242

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	0.027918300885081297	0.014129019985447857	0.02920575378432857	0.03581491191402242

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