QC Report

	general
Report generated at	2021-08-27 17:29:52
Title	arid-1_RW12194_L4larva_1_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	12052162	14237678	15170128
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	11882233	14090090	15033156
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	98.6	99.0	99.1
Paired Reads	12052162	14237678	15170128
Paired Reads (QC-failed)	0	0	0
Read1	6026081	7118839	7585064
Read1 (QC-failed)	0	0	0
Read2	6026081	7118839	7585064
Read2 (QC-failed)	0	0	0
Properly Paired Reads	11842348	14043102	14977832
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.3	98.6	98.7
With itself	11870184	14078648	15020406
With itself (QC-failed)	0	0	0
Singletons	12049	11442	12750
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	2385	3254	10969
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	5424239	6427502	6877090
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1003877	1230434	1239890
Paired Optical Duplicate Reads	100884	127101	157711
% Duplicate Reads	18.507199999999997	19.1433	18.0293

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	8840724	10394136	11274400
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	8840724	10394136	11274400
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	8840724	10394136	11274400
Paired Reads (QC-failed)	0	0	0
Read1	4420362	5197068	5637200
Read1 (QC-failed)	0	0	0
Read2	4420362	5197068	5637200
Read2 (QC-failed)	0	0	0
Properly Paired Reads	8840724	10394136	11274400
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	8840724	10394136	11274400
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	5320270	6314797	6800146
Distinct Fragments	4351603	5124246	5584472
Positions with Two Read	699338	847688	892537
NRF = Distinct/Total	0.817929	0.811466	0.821228
PBC1 = OneRead/Distinct	0.810625	0.803677	0.813137
PBC2 = OneRead/TwoRead	5.04408	4.858199	5.087677

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	56418	2330
N1	28244	1230
N2	29869	1257
Np	49252	2244
N optimal	56418	2330
N conservative	56418	2330
Optimal Set	rep1_vs_rep2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.1454966295784943	1.0383244206773619
Self Consistency Ratio	1.057534343577397	1.0219512195121951
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	91227	116847

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	61.0	68.0	68.0
25 percentile	244.0	244.0	270.0	270.0
50 percentile (median)	244.0	244.0	270.0	270.0
75 percentile	244.0	244.0	270.0	270.0
Max size	953.0	795.0	1104.0	1104.0
Mean	243.93095245925	243.92611705906015	261.9699570815451	269.6729058102024

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	4999182	5941408
Estimated Fragment Length	135	155
Cross-correlation at Estimated Fragment Length	0.58399153631552	0.62236646073088
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.5835678	0.6217428
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.5778203	0.616266
NSC (Normalized Strand Cross-correlation coeff.)	1.01068	1.009899
RSC (Relative Strand Cross-correlation coeff.)	1.07372	1.11387

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	0.385445607955655	0.39165704538226886
Synthetic AUC	0.4978395304037185	0.49800733263002317
X-intercept	0.02009707265281359	0.019883528782520535
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5771512050260643	0.5673301827296894
Synthetic Elbow Point	0.5029213152631986	0.5003887417165729
JS Distance	0.07355710093052896	0.06323424339672908
Synthetic JS Distance	0.17955957220722948	0.17060075969239483
% Genome Enriched	38.35327739947472	39.346356183192704
Diff. Enrichment	12.34957497376975	11.486702739003823
CHANCE Divergence	0.10516799487659044	0.09774987753740871

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	0.4202012188142057	0.48756750921865943	0.3804937242696413	0.3784735931875434	0.39181089693559035	0.37466837070440484	0.4636562990320699	0.40567823212646204	0.42780358162211735

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	0.2800331793420904	0.1700375444364059	0.16870983793169533	0.25327088421750926

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	0.0377661183912958	0.029656055318546308	0.02643423176298636	0.03709889232362492

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