QC Report

	general
Report generated at	2021-08-30 08:44:26
Title	F39B2.1_RW12232_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	8770112	12035674	10810052
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	8655001	11983041	10752580
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	98.7	99.6	99.5
Paired Reads	8770112	12035674	10810052
Paired Reads (QC-failed)	0	0	0
Read1	4385056	6017837	5405026
Read1 (QC-failed)	0	0	0
Read2	4385056	6017837	5405026
Read2 (QC-failed)	0	0	0
Properly Paired Reads	8607466	11936684	10682742
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.1	99.2	98.8
With itself	8648248	11974690	10743602
With itself (QC-failed)	0	0	0
Singletons	6753	8351	8978
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	2392	2783	33075
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	3921085	5439916	4919964
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	489330	745736	606374
Paired Optical Duplicate Reads	25202	38956	35203
% Duplicate Reads	12.4795	13.7086	12.3248

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	6863510	9388360	8627180
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	6863510	9388360	8627180
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	6863510	9388360	8627180
Paired Reads (QC-failed)	0	0	0
Read1	3431755	4694180	4313590
Read1 (QC-failed)	0	0	0
Read2	3431755	4694180	4313590
Read2 (QC-failed)	0	0	0
Properly Paired Reads	6863510	9388360	8627180
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	6863510	9388360	8627180
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	3886396	5379992	4853314
Distinct Fragments	3404103	4647513	4257763
Positions with Two Read	392739	586261	489259
NRF = Distinct/Total	0.875902	0.863851	0.87729
PBC1 = OneRead/Distinct	0.872132	0.858962	0.873194
PBC2 = OneRead/TwoRead	7.559285	6.809319	7.598947

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	65115	567
N1	37551	209
N2	34636	272
Np	70278	630
N optimal	70278	630
N conservative	65115	567
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0792904860631192	1.1111111111111112
Self Consistency Ratio	1.084160988566809	1.3014354066985645
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	105545	145295

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	56.0	58.0	58.0	58.0
25 percentile	216.0	224.0	230.0	230.0
50 percentile (median)	216.0	224.0	230.0	230.0
75 percentile	216.0	224.0	230.0	230.0
Max size	383.0	456.0	478.0	478.0
Mean	215.99518688710975	223.99422554114045	228.30793650793652	229.98239847462932

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	3667818	5070577
Estimated Fragment Length	115	140
Cross-correlation at Estimated Fragment Length	0.534267018607065	0.607150986851944
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.5346148	0.6072301
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.5291389	0.6025437
NSC (Normalized Strand Cross-correlation coeff.)	1.009691	1.007646
RSC (Relative Strand Cross-correlation coeff.)	0.9364872	0.9831271

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	0.3942492809282617	0.4040759186352036
Synthetic AUC	0.4975339051058796	0.497896335417975
X-intercept	0.02054713890368703	0.01993459553182532
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5290060236756992	0.5259073922212978
Synthetic Elbow Point	0.5017545590805023	0.49814552416003793
JS Distance	0.05295348834494976	0.03886952303991985
Synthetic JS Distance	0.15768067480915532	0.14891868018965468
% Genome Enriched	43.755948354812254	43.34033667937644
Diff. Enrichment	11.811598472418023	10.251637857061652
CHANCE Divergence	0.10052791646611624	0.08716343442611833

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	0.43674563015133655	0.5412598153458112	0.45420857426926625	0.39361059865620834	0.45581734588201833	0.4036381221001325	0.5340560193996137	0.5320404935505276	0.47081972361577146

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	0.2642632509366614	0.1768946209738166	0.15872218364016719	0.28246952504542555

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	0.007374659039236716	0.00435666299021929	0.004804566505758195	0.007829929725010107

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