QC Report

	general
Report generated at	2021-08-31 14:15:02
Title	pbrm-1_RW12226_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	14731774	15468008	13494174
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14518412	15172872	13390027
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	98.6	98.1	99.2
Paired Reads	14731774	15468008	13494174
Paired Reads (QC-failed)	0	0	0
Read1	7365887	7734004	6747087
Read1 (QC-failed)	0	0	0
Read2	7365887	7734004	6747087
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14473266	15127210	13281848
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.2	97.8	98.4
With itself	14509516	15163710	13382382
With itself (QC-failed)	0	0	0
Singletons	8896	9162	7645
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	5495	4270	51532
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	6562343	6880028	6089599
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1013990	982261	795226
Paired Optical Duplicate Reads	43562	41903	41083
% Duplicate Reads	15.4516	14.277000000000001	13.058800000000002

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	11096706	11795534	10588746
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	11096706	11795534	10588746
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	11096706	11795534	10588746
Paired Reads (QC-failed)	0	0	0
Read1	5548353	5897767	5294373
Read1 (QC-failed)	0	0	0
Read2	5548353	5897767	5294373
Read2 (QC-failed)	0	0	0
Properly Paired Reads	11096706	11795534	10588746
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	11096706	11795534	10588746
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	6519759	6830155	6015250
Distinct Fragments	5514851	5857540	5232069
Positions with Two Read	750203	743944	614968
NRF = Distinct/Total	0.845867	0.8576	0.869801
PBC1 = OneRead/Distinct	0.842525	0.854752	0.867366
PBC2 = OneRead/TwoRead	6.193522	6.730001	7.379436

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	67180	2917
N1	35671	1370
N2	31808	2173
Np	67689	3243
N optimal	67689	3243
N conservative	67180	2917
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0075766597201548	1.1117586561535824
Self Consistency Ratio	1.121447434607646	1.5861313868613138
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	112920	103781

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	74.0	80.0	80.0
25 percentile	284.0	296.0	320.0	320.0
50 percentile (median)	284.0	296.0	320.0	320.0
75 percentile	284.0	296.0	320.0	320.0
Max size	560.0	569.0	818.0	818.0
Mean	283.81347856889835	295.55796340370586	301.358926919519	319.1188376250203

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	6146179	6443952
Estimated Fragment Length	155	155
Cross-correlation at Estimated Fragment Length	0.64445568057705	0.661217938199859
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.643139	0.6591066
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.637237	0.6514937
NSC (Normalized Strand Cross-correlation coeff.)	1.011328	1.014926
RSC (Relative Strand Cross-correlation coeff.)	1.223099	1.277339

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	0.3952003268799152	0.38872290038994145
Synthetic AUC	0.49808245866552153	0.49813980595187096
X-intercept	0.0196011120802007	0.019549220326399133
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5609478627582862	0.5909492798023324
Synthetic Elbow Point	0.5023137615050399	0.5012564988756008
JS Distance	0.06335719897264144	0.07776829718299734
Synthetic JS Distance	0.15860787850134278	0.17127454948061013
% Genome Enriched	41.10226068421273	38.1342519504314
Diff. Enrichment	11.306499547386133	12.012954505981554
CHANCE Divergence	0.09613811141958581	0.10235625850139288

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	0.5059283358502965	0.48367059939804335	0.4089766081976745	0.3797400982880303	0.3974457640755309	0.38205466273161737	0.4790065978689722	0.49358219316551055	0.4957903631606803

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	0.34659469759184774	0.2036268240322849	0.19906381516936833	0.34907575667562457

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	0.03636699597767628	0.01926562711492942	0.03234546227411154	0.03921970938623743

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