QC Report

	general
Report generated at	2021-09-01 16:45:21
Title	Y48G9A.11_RW12291_L4larva_1_2
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	27333138	34293882	29635194
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	27248629	34132827	29561574
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.7	99.5	99.8
Paired Reads	27333138	34293882	29635194
Paired Reads (QC-failed)	0	0	0
Read1	13666569	17146941	14817597
Read1 (QC-failed)	0	0	0
Read2	13666569	17146941	14817597
Read2 (QC-failed)	0	0	0
Properly Paired Reads	27145084	33976128	29449080
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.3	99.1	99.4
With itself	27228448	34086448	29532786
With itself (QC-failed)	0	0	0
Singletons	20181	46379	28788
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	7786	12278	15865
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	12486561	15645550	13568929
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1362830	3098073	1348665
Paired Optical Duplicate Reads	72415	311159	86869
% Duplicate Reads	10.9144	19.8016	9.9394

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	22247462	25094954	24440528
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	22247462	25094954	24440528
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	22247462	25094954	24440528
Paired Reads (QC-failed)	0	0	0
Read1	11123731	12547477	12220264
Read1 (QC-failed)	0	0	0
Read2	11123731	12547477	12220264
Read2 (QC-failed)	0	0	0
Properly Paired Reads	22247462	25094954	24440528
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	22247462	25094954	24440528
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	12389200	15511057	13370009
Distinct Fragments	11042403	12460288	12053489
Positions with Two Read	1110296	2122215	1124262
NRF = Distinct/Total	0.891293	0.803316	0.901532
PBC1 = OneRead/Distinct	0.889303	0.795596	0.899089
PBC2 = OneRead/TwoRead	8.844524	4.67123	9.639351

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	71717	2171
N1	60451	1358
N2	65792	1200
Np	72079	2228
N optimal	72079	2228
N conservative	71717	2171
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0050476177196481	1.0262551819438046
Self Consistency Ratio	1.0883525499991729	1.1316666666666666
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	115712	109970

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	75.0	81.0	81.0
25 percentile	290.0	300.0	324.0	324.0
50 percentile (median)	290.0	300.0	324.0	324.0
75 percentile	290.0	300.0	324.0	324.0
Max size	536.0	548.0	637.0	637.0
Mean	289.75878042035396	299.7563153587342	303.5094254937163	323.36318483885736

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	11664446	14621928
Estimated Fragment Length	165	180
Cross-correlation at Estimated Fragment Length	0.790496558594657	0.800203479591718
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7900537	0.7998321
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.785097	0.7949545
NSC (Normalized Strand Cross-correlation coeff.)	1.006878	1.006603
RSC (Relative Strand Cross-correlation coeff.)	1.089346	1.076133

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	0.42048974612980006	0.42034509807564735
Synthetic AUC	0.4986500201484063	0.49872929767761454
X-intercept	0.01863065020549833	0.018426949238517856
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5323964420231101	0.5315676586770621
Synthetic Elbow Point	0.49930630260193803	0.5001226072113196
JS Distance	0.04947550449068905	0.045322003963153064
Synthetic JS Distance	0.13033820616820602	0.1310075765351543
% Genome Enriched	42.059656424369024	42.096003067496916
Diff. Enrichment	7.467497306686788	7.644665017342772
CHANCE Divergence	0.06347547550241756	0.06498301325810488

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	0.48944436898015603	0.4737644866772818	0.48447121883195315	0.5048092533017392	0.5049149880480738	0.5017559706828688	0.4538066244865915	0.4819076844825423	0.48084833531506593

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	0.34218251556912516	0.287296096966027	0.3137036632942224	0.3437691688569506

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	0.020972820651992075	0.015435558447071401	0.013241944974276502	0.021393753964732178

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