QC Report

	general
Report generated at	2021-08-30 17:04:51
Title	grh-1_RW12208_L1larva_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	20414982	18401162	17749312
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	20344218	18316871	17555109
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.7	99.5	98.9
Paired Reads	20414982	18401162	17749312
Paired Reads (QC-failed)	0	0	0
Read1	10207491	9200581	8874656
Read1 (QC-failed)	0	0	0
Read2	10207491	9200581	8874656
Read2 (QC-failed)	0	0	0
Properly Paired Reads	20257234	18244144	17265662
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.2	99.1	97.3
With itself	20328762	18304640	17541084
With itself (QC-failed)	0	0	0
Singletons	15456	12231	14025
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	9696	10866	14863
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	9351676	8424106	7980379
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1217301	1077372	912869
Paired Optical Duplicate Reads	124513	108546	93399
% Duplicate Reads	13.016900000000001	12.789200000000001	11.4389

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	16268750	14693468	14135020
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	16268750	14693468	14135020
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	16268750	14693468	14135020
Paired Reads (QC-failed)	0	0	0
Read1	8134375	7346734	7067510
Read1 (QC-failed)	0	0	0
Read2	8134375	7346734	7067510
Read2 (QC-failed)	0	0	0
Properly Paired Reads	16268750	14693468	14135020
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	16268750	14693468	14135020
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	9326085	8402444	7825993
Distinct Fragments	8114679	7329734	6938390
Positions with Two Read	980580	871180	740339
NRF = Distinct/Total	0.870106	0.872334	0.886583
PBC1 = OneRead/Distinct	0.865661	0.868075	0.883172
PBC2 = OneRead/TwoRead	7.163677	7.303613	8.27701

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	87881	2389
N1	66534	1787
N2	54433	1487
Np	87461	2470
N optimal	87881	2470
N conservative	87881	2389
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0048021403825704	1.033905399748849
Self Consistency Ratio	1.222309995774622	1.2017484868863484
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	129004	133620

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	81.0	76.0	86.0	86.0
25 percentile	324.0	304.0	344.0	344.0
50 percentile (median)	324.0	304.0	344.0	344.0
75 percentile	324.0	304.0	344.0	344.0
Max size	659.0	488.0	819.0	819.0
Mean	323.5028526247248	303.67587935937735	312.5449392712551	343.1192976866444

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	8818027	7939065
Estimated Fragment Length	175	170
Cross-correlation at Estimated Fragment Length	0.73203505244897	0.711974572568454
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7282543	0.7089098
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7212347	0.7027816
NSC (Normalized Strand Cross-correlation coeff.)	1.014975	1.013081
RSC (Relative Strand Cross-correlation coeff.)	1.538609	1.500101

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	0.4114686931025663	0.4124114701434733
Synthetic AUC	0.49842318323463825	0.4983410303853186
X-intercept	0.018840047279813435	0.019045698495351884
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5549927323259751	0.5458003226527809
Synthetic Elbow Point	0.5004151174628397	0.5001825959952251
JS Distance	0.08308928539247787	0.08104810754906905
Synthetic JS Distance	0.1401316915866727	0.1363586760783342
% Genome Enriched	45.43434335367217	45.260038973900265
Diff. Enrichment	5.968527031136994	5.843158325656994
CHANCE Divergence	0.05087141815579237	0.04978825495162253

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	0.567680799077987	0.5726527597160861	0.5350935339108986	0.48366648363749115	0.5547207443375483	0.5092569024548868	0.5679191975200226	0.5712076847202817	0.5714402354146745

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	0.42205474426928974	0.3398495274683058	0.27819647478730003	0.42095017223895265

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	0.033243451744962196	0.029059946215904724	0.023563667882898712	0.033967753860527694

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