QC Report

	general
Report generated at	2023-07-21 16:58:49
Title	Y56A3A.28_RW12344_youngadult_1_1
Description	mkudron
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	10331956	8397104	12390886
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	9244630	7643185	11537483
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	89.5	91.0	93.10000000000001
Paired Reads	10331956	8397104	12390886
Paired Reads (QC-failed)	0	0	0
Read1	5165978	4198552	6195443
Read1 (QC-failed)	0	0	0
Read2	5165978	4198552	6195443
Read2 (QC-failed)	0	0	0
Properly Paired Reads	9180702	7570950	11368054
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	88.9	90.2	91.7
With itself	9235662	7633632	11513246
With itself (QC-failed)	0	0	0
Singletons	8968	9553	24237
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.2
Diff. Chroms	11221	12787	87539
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	4092664	3313320	5171258
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	542055	354048	429864
Paired Optical Duplicate Reads	40052	25052	32109
% Duplicate Reads	13.2446	10.6856	8.3126

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	7101218	5918544	9482788
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	7101218	5918544	9482788
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	7101218	5918544	9482788
Paired Reads (QC-failed)	0	0	0
Read1	3550609	2959272	4741394
Read1 (QC-failed)	0	0	0
Read2	3550609	2959272	4741394
Read2 (QC-failed)	0	0	0
Properly Paired Reads	7101218	5918544	9482788
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	7101218	5918544	9482788
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	4074981	3299239	5131422
Distinct Fragments	3537193	2948432	4707624
Positions with Two Read	428205	293102	369848
NRF = Distinct/Total	0.868027	0.89367	0.917411
PBC1 = OneRead/Distinct	0.864315	0.891307	0.91596
PBC2 = OneRead/TwoRead	7.139685	8.966019	11.658825

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	18809	1026
N1	21185	679
N2	22621	702
Np	18914	1026
N optimal	18914	1026
N conservative	18809	1026
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0055824339411983	1.0
Self Consistency Ratio	1.0677838092990324	1.0338733431516938
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	47084	54513

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	84.0	80.0	81.0	81.0
25 percentile	336.0	320.0	324.0	324.0
50 percentile (median)	336.0	320.0	324.0	324.0
75 percentile	336.0	320.0	324.0	324.0
Max size	880.0	929.0	1206.0	1206.0
Mean	335.9778693399032	319.90305064846916	321.01559454191033	323.8352014380882

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	3825905	3095123
Estimated Fragment Length	205	180
Cross-correlation at Estimated Fragment Length	0.541186234180075	0.501744926766615
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.5365806	0.495868
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.5280962	0.4863833
NSC (Normalized Strand Cross-correlation coeff.)	1.024787	1.031583
RSC (Relative Strand Cross-correlation coeff.)	1.542833	1.619621

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	0.3901801852610044	0.3801165852887263
Synthetic AUC	0.4976051907729075	0.4973738965619178
X-intercept	0.019521071344487852	0.02007174751896441
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5571745523760879	0.5627092469702835
Synthetic Elbow Point	0.5019166150761888	0.4985237006249109
JS Distance	0.07840289435992302	0.08970314589172249
Synthetic JS Distance	0.1691213817339739	0.18187424168154212
% Genome Enriched	38.73947031336667	39.41604383063116
Diff. Enrichment	11.386902042666946	12.813610880656146
CHANCE Divergence	0.09692753464272874	0.10899750860796818

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	0.2967945780568911	0.33971801172720856	0.392615071776399	0.41887700758835283	0.3861366841960588	0.4187786725924484	0.21814845770606253	0.32734664007734704	0.3036370870123566

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	0.1360019484227131	0.1556182333791189	0.1682172169371386	0.13641278542572438

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	0.02721593528360964	0.022217878679404012	0.02409241191752566	0.027200420407070422

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