QC Report

	general
Report generated at	2021-08-28 09:59:18
Title	B0019.2_RW12288_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	16073902	14459532	14379230
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	16032426	14410675	14346476
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.7	99.7	99.8
Paired Reads	16073902	14459532	14379230
Paired Reads (QC-failed)	0	0	0
Read1	8036951	7229766	7189615
Read1 (QC-failed)	0	0	0
Read2	8036951	7229766	7189615
Read2 (QC-failed)	0	0	0
Properly Paired Reads	15982220	14364534	14232744
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.4	99.3	99.0
With itself	16020822	14399382	14333888
With itself (QC-failed)	0	0	0
Singletons	11604	11293	12588
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	5786	4859	10238
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	7269003	6531404	6498067
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1296894	1097854	1015993
Paired Optical Duplicate Reads	78634	64303	62887
% Duplicate Reads	17.8414	16.808899999999998	15.635299999999999

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	11944218	10867100	10964148
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	11944218	10867100	10964148
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	11944218	10867100	10964148
Paired Reads (QC-failed)	0	0	0
Read1	5972109	5433550	5482074
Read1 (QC-failed)	0	0	0
Read2	5972109	5433550	5482074
Read2 (QC-failed)	0	0	0
Properly Paired Reads	11944218	10867100	10964148
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	11944218	10867100	10964148
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	7221301	6489061	6451554
Distinct Fragments	5940147	5404903	5447707
Positions with Two Read	919047	796615	758465
NRF = Distinct/Total	0.822587	0.832925	0.844402
PBC1 = OneRead/Distinct	0.817107	0.827891	0.839691
PBC2 = OneRead/TwoRead	5.281271	5.617107	6.031113

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	38919	900
N1	33542	524
N2	30097	496
Np	31862	866
N optimal	38919	900
N conservative	38919	900
Optimal Set	rep1_vs_rep2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.2214864101437448	1.0392609699769053
Self Consistency Ratio	1.1144632355384259	1.0564516129032258
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	92919	65776

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	65.0	62.0	68.0	68.0
25 percentile	260.0	244.0	270.0	270.0
50 percentile (median)	260.0	244.0	270.0	270.0
75 percentile	260.0	244.0	270.0	270.0
Max size	260.0	244.0	270.0	270.0
Mean	259.9335765559251	243.93611651666262	258.23777777777775	269.7331894447442

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	6769266	6082354
Estimated Fragment Length	175	155
Cross-correlation at Estimated Fragment Length	0.654857700688804	0.635547094455862
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6549812	0.6355256
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.650563	0.6310258
NSC (Normalized Strand Cross-correlation coeff.)	1.006601	1.007165
RSC (Relative Strand Cross-correlation coeff.)	0.9720497	1.004767

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	0.41100487202054076	0.4084097308413094
Synthetic AUC	0.4981526799003837	0.4980597873135666
X-intercept	0.019453412777913022	0.0196190331759607
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5144289288949727	0.5163804559948598
Synthetic Elbow Point	0.5002110996772946	0.5025057899364496
JS Distance	0.030947387747514373	0.034748024845642045
Synthetic JS Distance	0.13490233654709635	0.13771992048450019
% Genome Enriched	43.5988713867815	42.90605931205677
Diff. Enrichment	8.835443150730116	9.199585545267247
CHANCE Divergence	0.07510723773632944	0.07819384053616214

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	0.40952383822867267	0.3003712121909249	0.3845605656962112	0.3811221024928454	0.38518727390730373	0.38028342428062684	0.5487013946322611	0.3120747944441619	0.30222166928028177

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	0.18527316133158112	0.16655288776544433	0.14827276826384225	0.1559213281757766

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	0.009339267463633623	0.006332603775316224	0.00614671807565956	0.00909447669792688

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