QC Report

	general
Report generated at	2021-08-27 12:32:27
Title	aptf-2_RW12304_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	22371904	21535360	25207972
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	22329364	21197775	25162694
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.8	98.4	99.8
Paired Reads	22371904	21535360	25207972
Paired Reads (QC-failed)	0	0	0
Read1	11185952	10767680	12603986
Read1 (QC-failed)	0	0	0
Read2	11185952	10767680	12603986
Read2 (QC-failed)	0	0	0
Properly Paired Reads	22227184	21114138	24916154
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.4	98.0	98.8
With itself	22311782	21181878	25137726
With itself (QC-failed)	0	0	0
Singletons	17582	15897	24968
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	12927	9963	80535
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	10089656	9629502	11345691
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1747734	1716665	2079673
Paired Optical Duplicate Reads	161246	159427	216728
% Duplicate Reads	17.322000000000003	17.8271	18.330099999999998

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	16683844	15825674	18532036
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	16683844	15825674	18532036
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	16683844	15825674	18532036
Paired Reads (QC-failed)	0	0	0
Read1	8341922	7912837	9266018
Read1 (QC-failed)	0	0	0
Read2	8341922	7912837	9266018
Read2 (QC-failed)	0	0	0
Properly Paired Reads	16683844	15825674	18532036
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	16683844	15825674	18532036
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	10041129	9586545	11253875
Distinct Fragments	8309058	7883689	9202678
Positions with Two Read	1254670	1214220	1472169
NRF = Distinct/Total	0.827502	0.82237	0.817734
PBC1 = OneRead/Distinct	0.822485	0.817456	0.810956
PBC2 = OneRead/TwoRead	5.446909	5.307579	5.069366

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	65846	892
N1	37251	350
N2	35463	403
Np	62970	832
N optimal	65846	892
N conservative	65846	892
Optimal Set	rep1_vs_rep2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0456725424805462	1.0721153846153846
Self Consistency Ratio	1.0504187462989594	1.1514285714285715
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	113388	107381

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	69.0	74.0	74.0
25 percentile	276.0	276.0	296.0	296.0
50 percentile (median)	276.0	276.0	296.0	296.0
75 percentile	276.0	276.0	296.0	296.0
Max size	285.0	276.0	322.0	322.0
Mean	275.94562034783223	275.9141002598225	281.38677130044846	295.80203808887404

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	9446735	9015693
Estimated Fragment Length	160	175
Cross-correlation at Estimated Fragment Length	0.727171624544151	0.716061514078526
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7272796	0.7160549
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7232796	0.7120212
NSC (Normalized Strand Cross-correlation coeff.)	1.005381	1.005674
RSC (Relative Strand Cross-correlation coeff.)	0.9730104	1.001641

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	0.42270826737357725	0.4202209537751367
Synthetic AUC	0.49844015565643457	0.498398001385165
X-intercept	0.018846794188455963	0.018902689775499366
Synthetic X-intercept	0.0	0.0
Elbow Point	0.4948895463274603	0.502261775004292
Synthetic Elbow Point	0.5005388638920519	0.5006588550592682
JS Distance	0.03242455431019362	0.0373326491282714
Synthetic JS Distance	0.11928800612850424	0.12169493634671939
% Genome Enriched	44.73603309018753	44.20362762359912
Diff. Enrichment	7.10387157709913	7.501459842133568
CHANCE Divergence	0.060385319095856795	0.06375571384189782

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	0.4874690748726732	0.46882824706233683	0.39359035004163306	0.39797705955815094	0.40966206588841275	0.390886908309486	0.5532830108400869	0.45845352376780707	0.47137754988416314

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	0.30367540361564266	0.18230235190403363	0.176840430303316	0.29235948684320695

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	0.008073266420006596	0.0038483337533004986	0.0045466625939596635	0.007671660957877013

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