QC Report

	general
Report generated at	2021-09-01 03:21:15
Title	tbx-11_OP368_earlyembryonic_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	19544526	15350114	20519140
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	19490299	15304891	20489462
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.7	99.7	99.9
Paired Reads	19544526	15350114	20519140
Paired Reads (QC-failed)	0	0	0
Read1	9772263	7675057	10259570
Read1 (QC-failed)	0	0	0
Read2	9772263	7675057	10259570
Read2 (QC-failed)	0	0	0
Properly Paired Reads	19364068	15146112	20414152
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.1	98.7	99.5
With itself	19477576	15292370	20475864
With itself (QC-failed)	0	0	0
Singletons	12723	12521	13598
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	16547	9582	10424
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	8727375	6800312	9366238
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1132811	837394	1488310
Paired Optical Duplicate Reads	116378	78906	155763
% Duplicate Reads	12.98	12.3141	15.890199999999998

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	15189128	11925836	15755856
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	15189128	11925836	15755856
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	15189128	11925836	15755856
Paired Reads (QC-failed)	0	0	0
Read1	7594564	5962918	7877928
Read1 (QC-failed)	0	0	0
Read2	7594564	5962918	7877928
Read2 (QC-failed)	0	0	0
Properly Paired Reads	15189128	11925836	15755856
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	15189128	11925836	15755856
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	8672937	6763872	9309196
Distinct Fragments	7549363	5934447	7833137
Positions with Two Read	907242	673244	1124693
NRF = Distinct/Total	0.870451	0.877374	0.841441
PBC1 = OneRead/Distinct	0.866291	0.874126	0.835402
PBC2 = OneRead/TwoRead	7.208597	7.705162	5.818313

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	58694	882
N1	31771	561
N2	32069	467
Np	75793	1042
N optimal	75793	1042
N conservative	58694	882
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.2913244965413841	1.18140589569161
Self Consistency Ratio	1.0093796229265684	1.2012847965738758
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	121809	86153

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	80.0	68.0	82.0	82.0
25 percentile	320.0	270.0	330.0	330.0
50 percentile (median)	320.0	270.0	330.0	330.0
75 percentile	320.0	270.0	330.0	330.0
Max size	320.0	270.0	370.0	370.0
Mean	319.89312776560024	269.8467842094878	308.65834932821497	329.711305793411

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	8168185	6402997
Estimated Fragment Length	185	175
Cross-correlation at Estimated Fragment Length	0.716126562040853	0.667642110947015
Phantom Peak	50	55
Cross-correlation at Phantom Peak	0.7164597	0.6677741
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7121385	0.662865
NSC (Normalized Strand Cross-correlation coeff.)	1.0056	1.007207
RSC (Relative Strand Cross-correlation coeff.)	0.9228956	0.973117

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	0.41392885282418634	0.40497164716036754
Synthetic AUC	0.49836618086703866	0.4981410681368679
X-intercept	0.018278492533321623	0.01901098944964932
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5296272049753905	0.5301900500173644
Synthetic Elbow Point	0.5000938245848244	0.49947098750795443
JS Distance	0.02102777620858586	0.0328118374231186
Synthetic JS Distance	0.1341805759864073	0.14264219330257225
% Genome Enriched	41.31442280440536	43.43387369118569
Diff. Enrichment	6.764823418886834	7.857460903724594
CHANCE Divergence	0.05748305841819271	0.06683768465995653

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	0.5389707032556444	0.3922951816543511	0.38299091297406934	0.38817220025497584	0.3782772783269718	0.3946413484136458	0.5234687753964933	0.5338596060831945	0.5335726058865503

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	0.2920511714490936	0.17812707878951314	0.16472983529204996	0.36124986188438235

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	0.00992171702680483	0.009697528390043194	0.0062179288730785836	0.01113359398153728

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