QC Report

	general
Report generated at	2021-08-31 18:44:02
Title	rcor-1_RW12222_youngadult_1_2
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	11444326	16889852	13263232
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	10997197	16118476	13220116
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	96.1	95.39999999999999	99.7
Paired Reads	11444326	16889852	13263232
Paired Reads (QC-failed)	0	0	0
Read1	5722163	8444926	6631616
Read1 (QC-failed)	0	0	0
Read2	5722163	8444926	6631616
Read2 (QC-failed)	0	0	0
Properly Paired Reads	10923072	16009442	13160880
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	95.39999999999999	94.8	99.2
With itself	10989184	16105192	13212422
With itself (QC-failed)	0	0	0
Singletons	8013	13284	7694
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	2750	5576	17171
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	4973407	7282606	6047451
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	854023	1515156	1016587
Paired Optical Duplicate Reads	49533	89203	69917
% Duplicate Reads	17.1718	20.805100000000003	16.810200000000002

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	8238768	11534900	10061728
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	8238768	11534900	10061728
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	8238768	11534900	10061728
Paired Reads (QC-failed)	0	0	0
Read1	4119384	5767450	5030864
Read1 (QC-failed)	0	0	0
Read2	4119384	5767450	5030864
Read2 (QC-failed)	0	0	0
Properly Paired Reads	8238768	11534900	10061728
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	8238768	11534900	10061728
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	4895666	7149979	5958514
Distinct Fragments	4067965	5678249	4962521
Positions with Two Read	607770	994447	743321
NRF = Distinct/Total	0.830932	0.794163	0.832845
PBC1 = OneRead/Distinct	0.825535	0.786624	0.826426
PBC2 = OneRead/TwoRead	5.525521	4.491591	5.517342

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	31481	2344
N1	28613	1550
N2	25659	1482
Np	32107	2403
N optimal	32107	2403
N conservative	31481	2344
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0198850100060355	1.0251706484641638
Self Consistency Ratio	1.115125297166686	1.0458839406207827
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	70153	58250

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	60.0	65.0	70.0	70.0
25 percentile	240.0	260.0	280.0	280.0
50 percentile (median)	240.0	260.0	280.0	280.0
75 percentile	240.0	260.0	280.0	280.0
Max size	302.0	464.0	422.0	422.0
Mean	239.71500862400754	259.54650643776824	261.16562630045775	278.56884791478495

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	4625969	6750553
Estimated Fragment Length	135	125
Cross-correlation at Estimated Fragment Length	0.571484870438236	0.644744961558646
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.5704048	0.643806
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.5639085	0.6376928
NSC (Normalized Strand Cross-correlation coeff.)	1.013435	1.011059
RSC (Relative Strand Cross-correlation coeff.)	1.166256	1.153597

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	0.38260057138506737	0.39122553478335376
Synthetic AUC	0.4977461040375199	0.49809871438348885
X-intercept	0.020266036628925597	0.01966140792682197
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5757202664357238	0.5778314782074255
Synthetic Elbow Point	0.49824858459125426	0.5000254677111614
JS Distance	0.07191693740390086	0.06096173732194127
Synthetic JS Distance	0.18167091464157253	0.17440213542502636
% Genome Enriched	38.26760906264592	37.7621554314814
Diff. Enrichment	12.630439794784765	11.295960311842968
CHANCE Divergence	0.1075496869598705	0.09629429377804502

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	0.3449560662467981	0.3010158735663075	0.3914243003322827	0.3395096619823319	0.39141726044476555	0.3466830228263791	0.474068392369084	0.31146472166924216	0.3378235135737082

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	0.18500745536943372	0.16814285825259312	0.15813539779278538	0.1891127634994175

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	0.03663634890602998	0.02937526581644246	0.030552843977841162	0.03907160775633534

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