QC Report

	general
Report generated at	2022-07-25 10:33:36
Title	bed-2_RW12335_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	11913198	14731476	17133844
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	11851670	14603193	17081311
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.5	99.1	99.7
Paired Reads	11913198	14731476	17133844
Paired Reads (QC-failed)	0	0	0
Read1	5956599	7365738	8566922
Read1 (QC-failed)	0	0	0
Read2	5956599	7365738	8566922
Read2 (QC-failed)	0	0	0
Properly Paired Reads	11798762	14549054	16918806
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.0	98.8	98.7
With itself	11830366	14586370	17058076
With itself (QC-failed)	0	0	0
Singletons	21304	16823	23235
Singletons (QC-failed)	0	0	0
% Singleton	0.2	0.1	0.1
Diff. Chroms	5888	6520	60472
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	5386150	6643824	7692866
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	923424	1255230	1376922
Paired Optical Duplicate Reads	53967	75260	90840
% Duplicate Reads	17.1444	18.8932	17.8987

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	8925452	10777188	12631888
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	8925452	10777188	12631888
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	8925452	10777188	12631888
Paired Reads (QC-failed)	0	0	0
Read1	4462726	5388594	6315944
Read1 (QC-failed)	0	0	0
Read2	4462726	5388594	6315944
Read2 (QC-failed)	0	0	0
Properly Paired Reads	8925452	10777188	12631888
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	8925452	10777188	12631888
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	5353797	6594333	7609521
Distinct Fragments	4444426	5358130	6260126
Positions with Two Read	661368	863774	973591
NRF = Distinct/Total	0.830145	0.812536	0.82267
PBC1 = OneRead/Distinct	0.825358	0.80691	0.816607
PBC2 = OneRead/TwoRead	5.546446	5.00539	5.25073

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	53673	615
N1	33342	238
N2	33452	256
Np	54434	626
N optimal	54434	626
N conservative	53673	615
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0141784509902558	1.0178861788617886
Self Consistency Ratio	1.003299142223022	1.0756302521008403
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	94623	94789

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	74.0	76.0	88.0	88.0
25 percentile	296.0	304.0	320.0	320.0
50 percentile (median)	296.0	304.0	320.0	320.0
75 percentile	296.0	304.0	320.0	320.0
Max size	296.0	304.0	320.0	320.0
Mean	295.96607590120794	303.96658895019465	310.7332268370607	319.89343057647795

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	5003998	6174210
Estimated Fragment Length	195	195
Cross-correlation at Estimated Fragment Length	0.588605444750508	0.630967814137739
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.5887215	0.6307592
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.5849185	0.626931
NSC (Normalized Strand Cross-correlation coeff.)	1.006303	1.006439
RSC (Relative Strand Cross-correlation coeff.)	0.9694935	1.0545

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	0.40740440499871083	0.4101072295978098
Synthetic AUC	0.49786711183679927	0.49805925889928754
X-intercept	0.019575836911926693	0.01913084082310308
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5148983892338883	0.518242844143612
Synthetic Elbow Point	0.5005223762282668	0.5013882079997033
JS Distance	0.04406062675323893	0.03701402852233797
Synthetic JS Distance	0.13670196233345047	0.1362483420862665
% Genome Enriched	45.133778196388946	45.37982311904344
Diff. Enrichment	9.748254751500763	9.290800163251017
CHANCE Divergence	0.08299055894511807	0.07909242589910859

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	0.45893967050632284	0.4566307092350992	0.4296817684975506	0.4162130232858516	0.43036924068383314	0.4078256777185292	0.5426875281688139	0.4697732892647889	0.452184681849742

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	0.2765016261780147	0.18625185592841684	0.18711921885374924	0.28018818797886985

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	0.006346357645472891	0.0031098705141207415	0.0031659464416877573	0.0065352155853225765

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