QC Report

	general
Report generated at	2021-08-28 09:07:04
Title	C06A6.2_OP810_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	10475962	11315830	12156752
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	10383862	11198857	12079126
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.1	99.0	99.4
Paired Reads	10475962	11315830	12156752
Paired Reads (QC-failed)	0	0	0
Read1	5237981	5657915	6078376
Read1 (QC-failed)	0	0	0
Read2	5237981	5657915	6078376
Read2 (QC-failed)	0	0	0
Properly Paired Reads	10336694	11128040	12010880
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.7	98.3	98.8
With itself	10372494	11188174	12066032
With itself (QC-failed)	0	0	0
Singletons	11368	10683	13094
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	2491	2872	8194
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	4752692	5118744	5520194
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	729705	778890	890847
Paired Optical Duplicate Reads	71503	76747	93109
% Duplicate Reads	15.3535	15.2164	16.137999999999998

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	8045974	8679708	9258694
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	8045974	8679708	9258694
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	8045974	8679708	9258694
Paired Reads (QC-failed)	0	0	0
Read1	4022987	4339854	4629347
Read1 (QC-failed)	0	0	0
Read2	4022987	4339854	4629347
Read2 (QC-failed)	0	0	0
Properly Paired Reads	8045974	8679708	9258694
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	8045974	8679708	9258694
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	4693366	5064185	5440253
Distinct Fragments	3978244	4298820	4568556
Positions with Two Read	544448	586610	658926
NRF = Distinct/Total	0.847631	0.848867	0.839769
PBC1 = OneRead/Distinct	0.843252	0.8442	0.834017
PBC2 = OneRead/TwoRead	6.161588	6.186499	5.782522

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	22601	1346
N1	24926	748
N2	22615	790
Np	20870	1338
N optimal	22601	1346
N conservative	22601	1346
Optimal Set	rep1_vs_rep2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0829420220412074	1.0059790732436473
Self Consistency Ratio	1.1021888127349104	1.0561497326203209
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	52104	47820

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	72.0	75.0	80.0	80.0
25 percentile	290.0	300.0	320.0	320.0
50 percentile (median)	290.0	300.0	320.0	320.0
75 percentile	290.0	300.0	320.0	320.0
Max size	332.0	373.0	480.0	480.0
Mean	289.6920581913097	299.57768716018404	298.3922734026746	318.71496836423165

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	4429113	4795117
Estimated Fragment Length	155	165
Cross-correlation at Estimated Fragment Length	0.573104888761086	0.59296732223342
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.5724419	0.5922663
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.5662354	0.5858575
NSC (Normalized Strand Cross-correlation coeff.)	1.012132	1.012136
RSC (Relative Strand Cross-correlation coeff.)	1.106819	1.109385

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	0.3830044848709866	0.3856439874827087
Synthetic AUC	0.49775084515519147	0.49783537297475505
X-intercept	0.01962865780048089	0.0195847592062336
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5769053486446309	0.5785774860073231
Synthetic Elbow Point	0.49952671790106273	0.4989431673365456
JS Distance	0.06577955182515466	0.06613208203824762
Synthetic JS Distance	0.18583864549403536	0.18212590603252313
% Genome Enriched	40.242240424619126	39.98683042172581
Diff. Enrichment	11.207225583120822	10.778702375749694
CHANCE Divergence	0.09528591657814788	0.09163638484020534

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	0.2911422532561005	0.2741898690601112	0.3754395986266924	0.3540994697056629	0.37436819317790315	0.3541040781556246	0.527579204244108	0.2614043168578337	0.27424929808533943

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	0.14481729354892672	0.15580450545825775	0.14644075584109512	0.13634953719674928

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	0.019432750186210643	0.01294448627350772	0.014046555483202891	0.01938366399648158

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