QC Report

	general
Report generated at	2021-09-01 12:11:01
Title	Y53F4B.3_RW12270_youngadult_1_3
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	17550002	16257114	15285398
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	17478024	16217304	15254430
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.6	99.8	99.8
Paired Reads	17550002	16257114	15285398
Paired Reads (QC-failed)	0	0	0
Read1	8775001	8128557	7642699
Read1 (QC-failed)	0	0	0
Read2	8775001	8128557	7642699
Read2 (QC-failed)	0	0	0
Properly Paired Reads	17422482	16076684	15172934
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.3	98.9	99.3
With itself	17464034	16202006	15239498
With itself (QC-failed)	0	0	0
Singletons	13990	15298	14932
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	6458	26327	20960
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	7873172	6493876	6914199
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1399464	1122039	1013123
Paired Optical Duplicate Reads	166130	119463	129383
% Duplicate Reads	17.7751	17.278399999999998	14.6528

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	12947416	10743674	11802152
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	12947416	10743674	11802152
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	12947416	10743674	11802152
Paired Reads (QC-failed)	0	0	0
Read1	6473708	5371837	5901076
Read1 (QC-failed)	0	0	0
Read2	6473708	5371837	5901076
Read2 (QC-failed)	0	0	0
Properly Paired Reads	12947416	10743674	11802152
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	12947416	10743674	11802152
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	7823774	6457473	6870330
Distinct Fragments	6444091	5350498	5871840
Positions with Two Read	1012711	814868	783517
NRF = Distinct/Total	0.823655	0.828575	0.854666
PBC1 = OneRead/Distinct	0.816365	0.822704	0.849304
PBC2 = OneRead/TwoRead	5.1947	5.40195	6.364863

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	9520	437
N1	15930	287
N2	22490	248
Np	7365	465
N optimal	9520	465
N conservative	9520	437
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.2926001357773251	1.0640732265446224
Self Consistency Ratio	1.4118016321406153	1.157258064516129
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	23657	39791

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	65.0	59.0	65.0	65.0
25 percentile	260.0	236.0	260.0	260.0
50 percentile (median)	260.0	236.0	260.0	260.0
75 percentile	260.0	236.0	260.0	260.0
Max size	260.0	387.0	260.0	260.0
Mean	259.8718772456355	235.88135508029453	247.81505376344086	259.4778361344538

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7329533	5972596
Estimated Fragment Length	170	145
Cross-correlation at Estimated Fragment Length	0.671712966505753	0.626500054019563
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6719124	0.6260943
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6677792	0.6222753
NSC (Normalized Strand Cross-correlation coeff.)	1.005891	1.006789
RSC (Relative Strand Cross-correlation coeff.)	0.9517549	1.106236

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	0.41164288081095407	0.41039849644691123
Synthetic AUC	0.4982217999910886	0.4980344628558148
X-intercept	0.01929671189458263	0.019679931659141985
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5129775776519008	0.5099138154716997
Synthetic Elbow Point	0.5003964709651274	0.5001854763707289
JS Distance	0.027831125606459364	0.03092696007837283
Synthetic JS Distance	0.1341550119384542	0.13414541734643032
% Genome Enriched	42.23740464414452	42.69128055279451
Diff. Enrichment	7.602107759469284	7.943917081416874
CHANCE Divergence	0.06459786042443323	0.06751123211278585

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	0.12485124444908544	0.1862904626480662	0.32355212808486267	0.3596472939057358	0.3158767741764071	0.35944749616332294	0.568617864353223	0.13088514450916824	0.118555973452971

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	0.051804708014700884	0.08621534984277944	0.10976301030727477	0.04206062279109995

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	0.004763900690090663	0.0036624296307463974	0.003736059005513384	0.005123487353262344

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