QC Report

	general
Report generated at	2021-08-29 15:13:44
Title	ets-5_OP809_L1larva_1_4
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	16717286	15684140	13844212
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	16580668	15613052	13637689
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.2	99.5	98.5
Paired Reads	16717286	15684140	13844212
Paired Reads (QC-failed)	0	0	0
Read1	8358643	7842070	6922106
Read1 (QC-failed)	0	0	0
Read2	8358643	7842070	6922106
Read2 (QC-failed)	0	0	0
Properly Paired Reads	16524810	15544548	13398786
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.8	99.1	96.8
With itself	16570478	15600634	13614644
With itself (QC-failed)	0	0	0
Singletons	10190	12418	23045
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.2
Diff. Chroms	9125	14794	50122
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	7582282	7155546	6129928
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	800210	1080443	975592
Paired Optical Duplicate Reads	58613	126316	122010
% Duplicate Reads	10.553700000000001	15.0994	15.915199999999999

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	13564144	12150206	10308672
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	13564144	12150206	10308672
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	13564144	12150206	10308672
Paired Reads (QC-failed)	0	0	0
Read1	6782072	6075103	5154336
Read1 (QC-failed)	0	0	0
Read2	6782072	6075103	5154336
Read2 (QC-failed)	0	0	0
Properly Paired Reads	13564144	12150206	10308672
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	13564144	12150206	10308672
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	7574272	7141334	6063817
Distinct Fragments	6777699	6070186	5107705
Positions with Two Read	670324	833024	728193
NRF = Distinct/Total	0.894832	0.850007	0.842325
PBC1 = OneRead/Distinct	0.892212	0.844267	0.836447
PBC2 = OneRead/TwoRead	9.021224	6.15211	5.867022

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	91377	177
N1	73698	21
N2	59129	26
Np	93585	250
N optimal	93585	250
N conservative	91377	177
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0241636297974326	1.4124293785310735
Self Consistency Ratio	1.246393478665291	1.2380952380952381
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	136553	140903

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	304.0	86.0	85.0	85.0
25 percentile	304.0	290.0	310.0	310.0
50 percentile (median)	304.0	290.0	310.0	310.0
75 percentile	304.0	290.0	310.0	310.0
Max size	304.0	290.0	310.0	310.0
Mean	304.0	289.99841735094355	309.1	309.9975957685526

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7153875	6734434
Estimated Fragment Length	185	175
Cross-correlation at Estimated Fragment Length	0.697259445964488	0.665917471838106
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6978172	0.666589
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6941242	0.663186
NSC (Normalized Strand Cross-correlation coeff.)	1.004517	1.004119
RSC (Relative Strand Cross-correlation coeff.)	0.8489798	0.8026776

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	0.4229139759609008	0.4198691261442631
Synthetic AUC	0.49827104464260363	0.4981767372212498
X-intercept	0.01844734205810394	0.01881253716808155
Synthetic X-intercept	0.0	0.0
Elbow Point	0.48041516497639203	0.4981420948230101
Synthetic Elbow Point	0.4988502587486416	0.5016443988644691
JS Distance	0.05707068847935415	0.04870659500525597
Synthetic JS Distance	0.11333467389747197	0.11716652008631746
% Genome Enriched	49.37238326727892	47.48833570809935
Diff. Enrichment	6.8194893712162035	6.5019909822779
CHANCE Divergence	0.05842814837642559	0.0555292922404244

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	0.5771625544523856	0.5870583593397511	0.5688854379605525	0.5367042276148688	0.5691865258876638	0.5135294847724368	0.588161046264051	0.5860076894024007	0.5864336128608044

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	0.4052973923120748	0.3466754702692628	0.27976579162526133	0.4151107844452611

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	0.0015769016133015223	0.00032114079591015845	0.00034493242336796595	0.0021062558454714975

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