QC Report

	general
Report generated at	2022-06-01 00:25:58
Title	madf-8_RW12322_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	15184914	14920458	13135130
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	15098970	14539032	13084317
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.4	97.39999999999999	99.6
Paired Reads	15184914	14920458	13135130
Paired Reads (QC-failed)	0	0	0
Read1	7592457	7460229	6567565
Read1 (QC-failed)	0	0	0
Read2	7592457	7460229	6567565
Read2 (QC-failed)	0	0	0
Properly Paired Reads	15028264	14478726	13025112
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.0	97.0	99.2
With itself	15078060	14519818	13066482
With itself (QC-failed)	0	0	0
Singletons	20910	19214	17835
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	3906	3759	8573
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	6883504	6626323	5994039
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1001422	921324	653543
Paired Optical Duplicate Reads	109135	99979	83143
% Duplicate Reads	14.5481	13.904	10.9032

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	11764164	11409998	10680992
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	11764164	11409998	10680992
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	11764164	11409998	10680992
Paired Reads (QC-failed)	0	0	0
Read1	5882082	5704999	5340496
Read1 (QC-failed)	0	0	0
Read2	5882082	5704999	5340496
Read2 (QC-failed)	0	0	0
Properly Paired Reads	11764164	11409998	10680992
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	11764164	11409998	10680992
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	6821828	6570646	5915185
Distinct Fragments	5844340	5670036	5277454
Positions with Two Read	758743	710721	532286
NRF = Distinct/Total	0.856712	0.862934	0.892187
PBC1 = OneRead/Distinct	0.852576	0.858925	0.889589
PBC2 = OneRead/TwoRead	6.567105	6.852388	8.820007

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	31349	1977
N1	30316	1347
N2	25706	1608
Np	23646	1972
N optimal	31349	1977
N conservative	31349	1977
Optimal Set	rep1_vs_rep2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.3257633426372326	1.0025354969574036
Self Consistency Ratio	1.1793355636816307	1.1937639198218264
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	84052	51402

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	62.0	66.0	69.0	69.0
25 percentile	250.0	264.0	270.0	276.0
50 percentile (median)	250.0	264.0	276.0	276.0
75 percentile	250.0	264.0	276.0	276.0
Max size	350.0	378.0	396.0	396.0
Mean	249.63288202541284	263.07982179681727	246.84066767830046	274.14906376598935

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	6418928	6169188
Estimated Fragment Length	150	155
Cross-correlation at Estimated Fragment Length	0.661570689707553	0.655867157553493
Phantom Peak	50	55
Cross-correlation at Phantom Peak	0.658258	0.6506596
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.651195	0.642335
NSC (Normalized Strand Cross-correlation coeff.)	1.015933	1.021067
RSC (Relative Strand Cross-correlation coeff.)	1.469026	1.625559

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	0.40552827480664666	0.4000841208913824
Synthetic AUC	0.4981316101016412	0.49810322088364267
X-intercept	0.019705908180127248	0.019564210845633725
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5372783733944295	0.5577187128293964
Synthetic Elbow Point	0.49845891787867	0.5022492165853698
JS Distance	0.05494756440701281	0.07035728757284344
Synthetic JS Distance	0.14986633029631694	0.15932705492104954
% Genome Enriched	41.87834784899455	39.79619532678199
Diff. Enrichment	9.442579439999632	10.2047978256321
CHANCE Divergence	0.08026079780661323	0.08683480593005777

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	0.37402725769548945	0.26516376251774976	0.37595922668198095	0.3535065731814198	0.3565779939824028	0.35119363757883876	0.5340753206092199	0.2766255559423848	0.2473103663735816

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	0.166906747264475	0.15761196460708982	0.15025804561928932	0.13404963683260693

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	0.02830406553643666	0.020780992172499464	0.02799939141093627	0.028317874018486622

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