QC Report

	general
Report generated at	2021-09-01 15:18:51
Title	Y67H2A.10_RW12295_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	17705854	16466650	17592722
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	17635788	16410211	17562327
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.6	99.7	99.8
Paired Reads	17705854	16466650	17592722
Paired Reads (QC-failed)	0	0	0
Read1	8852927	8233325	8796361
Read1 (QC-failed)	0	0	0
Read2	8852927	8233325	8796361
Read2 (QC-failed)	0	0	0
Properly Paired Reads	17576042	16349452	17459148
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.3	99.3	99.2
With itself	17624250	16396170	17552354
With itself (QC-failed)	0	0	0
Singletons	11538	14041	9973
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	5058	6988	24673
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	8038083	7474030	7957891
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1065199	988642	846443
Paired Optical Duplicate Reads	64157	99621	53228
% Duplicate Reads	13.2519	13.2277	10.6365

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	13945768	12970776	14222896
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	13945768	12970776	14222896
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	13945768	12970776	14222896
Paired Reads (QC-failed)	0	0	0
Read1	6972884	6485388	7111448
Read1 (QC-failed)	0	0	0
Read2	6972884	6485388	7111448
Read2 (QC-failed)	0	0	0
Properly Paired Reads	13945768	12970776	14222896
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	13945768	12970776	14222896
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	7991013	7437850	7898363
Distinct Fragments	6935861	6458681	7061811
Positions with Two Read	842002	787468	697822
NRF = Distinct/Total	0.867958	0.868353	0.894085
PBC1 = OneRead/Distinct	0.864081	0.864032	0.891832
PBC2 = OneRead/TwoRead	7.117737	7.08665	9.025154

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	15592	709
N1	20905	325
N2	25612	414
Np	16535	683
N optimal	16535	709
N conservative	15592	709
Optimal Set	pooled-pr1_vs_pooled-pr2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.060479733196511	1.0380673499267936
Self Consistency Ratio	1.2251614446304713	1.2738461538461539
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	34569	49017

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	66.0	75.0	75.0
25 percentile	270.0	264.0	296.0	296.0
50 percentile (median)	270.0	264.0	296.0	296.0
75 percentile	270.0	264.0	296.0	296.0
Max size	270.0	264.0	297.0	297.0
Mean	269.83956724232695	263.8846930656711	284.07052186177714	295.4867251285153

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7514064	6991229
Estimated Fragment Length	160	165
Cross-correlation at Estimated Fragment Length	0.697578575447317	0.683044500507318
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6974979	0.6829278
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6933319	0.6784646
NSC (Normalized Strand Cross-correlation coeff.)	1.006125	1.00675
RSC (Relative Strand Cross-correlation coeff.)	1.019371	1.026142

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	0.41496608641409904	0.412526189338934
Synthetic AUC	0.4982936465295227	0.4982287427601498
X-intercept	0.019193693244187206	0.01928550044905698
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5105737950304361	0.5107234806905498
Synthetic Elbow Point	0.5016647244369051	0.5031317734311621
JS Distance	0.023250289786356196	0.02876585934095733
Synthetic JS Distance	0.12962214176968642	0.13110292780802457
% Genome Enriched	41.801417024249076	41.10468017163956
Diff. Enrichment	6.294911588152435	6.586235067366397
CHANCE Divergence	0.05348184619624776	0.055962591332755655

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	0.1756748714018475	0.2385491816372436	0.34898587155615957	0.3652533973295044	0.3418954051150141	0.36451219263982354	0.5740732539808974	0.2231083604195249	0.2008254848765131

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	0.08601683782286462	0.1100977730304993	0.13158264393741748	0.09054282748929432

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	0.007485879316453108	0.0040653193140743485	0.005091522666030159	0.007263005235739031

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