QC Report

	general
Report generated at	2021-09-01 19:05:56
Title	Y56A3A.18_RW12265_youngadult_2_5
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	14590286	10981600	11051710
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	13448674	10175995	11022264
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	92.2	92.7	99.7
Paired Reads	14590286	10981600	11051710
Paired Reads (QC-failed)	0	0	0
Read1	7295143	5490800	5525855
Read1 (QC-failed)	0	0	0
Read2	7295143	5490800	5525855
Read2 (QC-failed)	0	0	0
Properly Paired Reads	13363620	10114434	10957044
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	91.60000000000001	92.10000000000001	99.1
With itself	13436704	10167026	11015960
With itself (QC-failed)	0	0	0
Singletons	11970	8969	6304
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	4651	4199	27363
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	6125621	4628488	5053015
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	835532	511012	530536
Paired Optical Duplicate Reads	60610	37311	41808
% Duplicate Reads	13.639999999999999	11.040600000000001	10.4994

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	10580178	8234952	9044958
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	10580178	8234952	9044958
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	10580178	8234952	9044958
Paired Reads (QC-failed)	0	0	0
Read1	5290089	4117476	4522479
Read1 (QC-failed)	0	0	0
Read2	5290089	4117476	4522479
Read2 (QC-failed)	0	0	0
Properly Paired Reads	10580178	8234952	9044958
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	10580178	8234952	9044958
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	6016281	4569449	4949675
Distinct Fragments	5204942	4068003	4435377
Positions with Two Read	639141	411113	432840
NRF = Distinct/Total	0.865143	0.890261	0.896095
PBC1 = OneRead/Distinct	0.861595	0.888379	0.89363
PBC2 = OneRead/TwoRead	7.01653	8.790593	9.15716

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	70910	1687
N1	34780	817
N2	33977	754
Np	71132	1826
N optimal	71132	1826
N conservative	70910	1687
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0031307290932168	1.0823947836395968
Self Consistency Ratio	1.0236336345174677	1.0835543766578248
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	120131	116102

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	61.0	64.0	75.0	75.0
25 percentile	244.0	256.0	300.0	300.0
50 percentile (median)	244.0	256.0	300.0	300.0
75 percentile	244.0	256.0	300.0	300.0
Max size	250.0	256.0	488.0	488.0
Mean	243.95116997277972	255.9457029164011	292.16538882803945	299.7974329415734

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	5668840	4305265
Estimated Fragment Length	125	150
Cross-correlation at Estimated Fragment Length	0.634528998838086	0.580112870520727
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.635058	0.5806037
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6288188	0.5749627
NSC (Normalized Strand Cross-correlation coeff.)	1.009081	1.008957
RSC (Relative Strand Cross-correlation coeff.)	0.9152181	0.9129876

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	0.38691648220247976	0.38397537928700587
Synthetic AUC	0.4980069509833323	0.497752485626145
X-intercept	0.01990704988136787	0.020036757002687932
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5830075689094025	0.5749717138700814
Synthetic Elbow Point	0.4997341595900482	0.5013685006942946
JS Distance	0.0654668466062351	0.07371147111375118
Synthetic JS Distance	0.17913622111685173	0.1772584519829151
% Genome Enriched	39.174344330501725	40.64302804267963
Diff. Enrichment	11.957682504057294	12.598807944418233
CHANCE Divergence	0.10175035316293252	0.1071472485439759

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	0.48388845631897687	0.49616269773035715	0.37831946148364204	0.41367624243590007	0.38641550008241826	0.4153828704769621	0.4803874860285313	0.4896819219764177	0.4878292616452038

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	0.3397894141576487	0.1766101666720541	0.18397107839851404	0.3409154760025575

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	0.020065287882677398	0.010957377087606655	0.010759261256167614	0.021178806630621206

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