QC Report

	general
Report generated at	2022-02-19 12:21:53
Title	F44E2.7_OP381_L4larva_1_6
Description	gevirl
Pipeline version	v2.1.2
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	17610688	22492188	21989024
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	17543894	22373463	21917912
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.6	99.5	99.7
Paired Reads	17610688	22492188	21989024
Paired Reads (QC-failed)	0	0	0
Read1	8805344	11246094	10994512
Read1 (QC-failed)	0	0	0
Read2	8805344	11246094	10994512
Read2 (QC-failed)	0	0	0
Properly Paired Reads	17488076	22297016	21778270
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.3	99.1	99.0
With itself	17521998	22340544	21888734
With itself (QC-failed)	0	0	0
Singletons	21896	32919	29178
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	5136	6646	45345
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	8002090	10200891	9974585
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1388579	2049283	1903961
Paired Optical Duplicate Reads	137472	201337	226213
% Duplicate Reads	17.3527	20.089299999999998	19.0881

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	13227022	16303216	16141248
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	13227022	16303216	16141248
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	13227022	16303216	16141248
Paired Reads (QC-failed)	0	0	0
Read1	6613511	8151608	8070624
Read1 (QC-failed)	0	0	0
Read2	6613511	8151608	8070624
Read2 (QC-failed)	0	0	0
Properly Paired Reads	13227022	16303216	16141248
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	13227022	16303216	16141248
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	7947474	10128932	9869255
Distinct Fragments	6585177	8120906	8008313
Positions with Two Read	1005717	1398094	1344638
NRF = Distinct/Total	0.828587	0.801753	0.81144
PBC1 = OneRead/Distinct	0.822118	0.793379	0.802138
PBC2 = OneRead/TwoRead	5.383018	4.608383	4.777326

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	82237	864
N1	42594	178
N2	47608	319
Np	81869	896
N optimal	82237	896
N conservative	82237	864
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.004494985892096	1.037037037037037
Self Consistency Ratio	1.11771611025027	1.7921348314606742
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	132768	134982

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	67.0	68.0	71.0	71.0
25 percentile	256.0	250.0	270.0	270.0
50 percentile (median)	256.0	250.0	270.0	270.0
75 percentile	256.0	250.0	270.0	270.0
Max size	256.0	250.0	270.0	270.0
Mean	255.99582730778502	249.9909765746544	267.02566964285717	269.96703430329416

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7491925	9552072
Estimated Fragment Length	165	150
Cross-correlation at Estimated Fragment Length	0.680318930162185	0.719722758574216
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6804659	0.7196744
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6763764	0.7158062
NSC (Normalized Strand Cross-correlation coeff.)	1.005829	1.005471
RSC (Relative Strand Cross-correlation coeff.)	0.9640651	1.012498

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	0.4140860302677555	0.41689407919689675
Synthetic AUC	0.49824463435794114	0.4984182801081556
X-intercept	0.01910202517395418	0.01883854896465826
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5096747665640706	0.5085689648977832
Synthetic Elbow Point	0.5009437929728059	0.4996456518099314
JS Distance	0.03318604832548	0.029328161871099413
Synthetic JS Distance	0.13179103713952556	0.1297060650193134
% Genome Enriched	45.016307580529904	44.41849602989257
Diff. Enrichment	8.687758141186958	8.287323548095477
CHANCE Divergence	0.07390112792389025	0.07044992484842275

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	0.5338398167025049	0.5274821237723895	0.43813967525877323	0.4384796226707663	0.4307201470928448	0.4447745769914353	0.5151794916112765	0.5308363900869075	0.5303467943838986

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	0.3476938790672801	0.2000517576821147	0.21434807709104756	0.3463472932388828

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	0.0071301152398433095	0.0019015618179209198	0.0031836050016144056	0.007290019132253522

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