QC Report

	general
Report generated at	2022-05-31 19:59:11
Title	ztf-6_RW12301_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	13041348	15561502	17390306
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	13006559	15470868	17356242
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.7	99.4	99.8
Paired Reads	13041348	15561502	17390306
Paired Reads (QC-failed)	0	0	0
Read1	6520674	7780751	8695153
Read1 (QC-failed)	0	0	0
Read2	6520674	7780751	8695153
Read2 (QC-failed)	0	0	0
Properly Paired Reads	12963212	15398836	17283110
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.4	99.0	99.4
With itself	12999516	15442868	17343572
With itself (QC-failed)	0	0	0
Singletons	7043	28000	12670
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.2	0.1
Diff. Chroms	4262	3764	14607
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	5931724	7039971	7948918
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	623118	922186	967418
Paired Optical Duplicate Reads	57133	102412	96569
% Duplicate Reads	10.5048	13.0993	12.1704

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	10617212	12235570	13963000
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	10617212	12235570	13963000
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	10617212	12235570	13963000
Paired Reads (QC-failed)	0	0	0
Read1	5308606	6117785	6981500
Read1 (QC-failed)	0	0	0
Read2	5308606	6117785	6981500
Read2 (QC-failed)	0	0	0
Properly Paired Reads	10617212	12235570	13963000
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	10617212	12235570	13963000
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	5895823	7000090	7876561
Distinct Fragments	5278192	6096471	6922054
Positions with Two Read	522235	723264	789609
NRF = Distinct/Total	0.895243	0.870913	0.878817
PBC1 = OneRead/Distinct	0.89244	0.867367	0.874556
PBC2 = OneRead/TwoRead	9.019826	7.311131	7.666735

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	50049	551
N1	32238	215
N2	36261	253
Np	52938	605
N optimal	52938	605
N conservative	50049	551
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0577234310375832	1.0980036297640654
Self Consistency Ratio	1.1247906197654942	1.1767441860465115
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	84801	105379

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	70.0	61.0	78.0	78.0
25 percentile	276.0	244.0	280.0	280.0
50 percentile (median)	276.0	244.0	280.0	280.0
75 percentile	276.0	244.0	280.0	280.0
Max size	276.0	244.0	280.0	280.0
Mean	275.9808610747515	243.98502547945986	274.87603305785126	279.9414409309003

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	5550113	6581034
Estimated Fragment Length	190	175
Cross-correlation at Estimated Fragment Length	0.643151339074603	0.670478234852016
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6433552	0.6707497
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6394499	0.6667973
NSC (Normalized Strand Cross-correlation coeff.)	1.005788	1.00552
RSC (Relative Strand Cross-correlation coeff.)	0.9477916	0.9313102

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	0.4138745396655291	0.41449744916759684
Synthetic AUC	0.498046177221606	0.4981700688995704
X-intercept	0.019395115097374734	0.019682509270457876
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5066479860454163	0.5012753116430564
Synthetic Elbow Point	0.5034686316190257	0.503152870504674
JS Distance	0.03495484353922512	0.034981095231151504
Synthetic JS Distance	0.12968483084925003	0.12855871066770164
% Genome Enriched	44.31697980656776	43.94256906441222
Diff. Enrichment	8.779171435164873	8.633325842888956
CHANCE Divergence	0.07464340049667181	0.07338661887340979

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	0.39641640385442056	0.4369087014336071	0.40348596222812544	0.40158433132509047	0.4024161898622727	0.40399644707953075	0.5440227364878377	0.4415372761585634	0.4172592568606533

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	0.23318193819903416	0.16677438483850562	0.1682596724141172	0.2450171712135529

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	0.005213238370715653	0.0025469963301100137	0.0027298278707081074	0.005622247654574397

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