QC Report

	general
Report generated at	2022-06-01 03:27:20
Title	sea-2_OP586_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	19463894	15434692	21991186
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	19342378	15339712	21917444
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.4	99.4	99.7
Paired Reads	19463894	15434692	21991186
Paired Reads (QC-failed)	0	0	0
Read1	9731947	7717346	10995593
Read1 (QC-failed)	0	0	0
Read2	9731947	7717346	10995593
Read2 (QC-failed)	0	0	0
Properly Paired Reads	19266116	15268364	21788074
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.0	98.9	99.1
With itself	19327070	15324196	21903180
With itself (QC-failed)	0	0	0
Singletons	15308	15516	14264
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	11264	12901	53071
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	8821996	6962015	10026667
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1558673	1059223	1650335
Paired Optical Duplicate Reads	77583	52375	101614
% Duplicate Reads	17.668	15.2143	16.4595

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	14526646	11805584	16752664
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14526646	11805584	16752664
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	14526646	11805584	16752664
Paired Reads (QC-failed)	0	0	0
Read1	7263323	5902792	8376332
Read1 (QC-failed)	0	0	0
Read2	7263323	5902792	8376332
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14526646	11805584	16752664
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	14526646	11805584	16752664
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	8746979	6912780	9922679
Distinct Fragments	7206809	5865657	8296767
Positions with Two Read	1113358	796983	1241261
NRF = Distinct/Total	0.82392	0.848524	0.836142
PBC1 = OneRead/Distinct	0.818198	0.84422	0.828582
PBC2 = OneRead/TwoRead	5.29623	6.213314	5.538362

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	55077	431
N1	34920	167
N2	35087	119
Np	54102	453
N optimal	55077	453
N conservative	55077	431
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0180215149162692	1.051044083526682
Self Consistency Ratio	1.0047823596792669	1.403361344537815
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	99503	95032

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	111.0	88.0	76.0	76.0
25 percentile	296.0	280.0	304.0	304.0
50 percentile (median)	296.0	280.0	304.0	304.0
75 percentile	296.0	280.0	304.0	304.0
Max size	296.0	280.0	304.0	304.0
Mean	295.9883320100902	279.99446502230825	298.24061810154524	303.95262995442744

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	8231612	6509505
Estimated Fragment Length	175	175
Cross-correlation at Estimated Fragment Length	0.701758272220012	0.659588115368188
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7012668	0.6588751
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6974922	0.6552998
NSC (Normalized Strand Cross-correlation coeff.)	1.006116	1.006544
RSC (Relative Strand Cross-correlation coeff.)	1.130198	1.199426

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	0.4149092856088177	0.4128196840749698
Synthetic AUC	0.4983314833217168	0.4981485083599566
X-intercept	0.018629697342264304	0.018833278778830724
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5164701373975107	0.5121071077863911
Synthetic Elbow Point	0.49993059099041914	0.5007297758380047
JS Distance	0.03192784272246017	0.03746555274612641
Synthetic JS Distance	0.13285379812348383	0.13268778259242078
% Genome Enriched	43.9306785249527	44.382749067916365
Diff. Enrichment	8.115355205453694	8.521671407420584
CHANCE Divergence	0.06898353478461235	0.07246853310048271

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	0.46227188299350036	0.44175095446358265	0.3961785265258716	0.4228614187997815	0.4013864454859636	0.41546729073292776	0.5334017665803465	0.44521201241125324	0.44845464652668204

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	0.27102508978540746	0.18647098580085175	0.18314672107707675	0.26710795097870554

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	0.00417112413190983	0.001969897249509625	0.0014428765235163293	0.004323484946014827

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