QC Report

	general
Report generated at	2021-09-01 02:42:44
Title	tab-1_OP787_midembryonic_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	19870374	19244226	20298684
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	19766735	19004191	20273862
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.5	98.8	99.9
Paired Reads	19870374	19244226	20298684
Paired Reads (QC-failed)	0	0	0
Read1	9935187	9622113	10149342
Read1 (QC-failed)	0	0	0
Read2	9935187	9622113	10149342
Read2 (QC-failed)	0	0	0
Properly Paired Reads	19576262	18377338	19971440
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.5	95.5	98.4
With itself	19755768	18983738	20261852
With itself (QC-failed)	0	0	0
Singletons	10967	20453	12010
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	7565	9808	93921
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	8893354	8288349	9200522
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1062184	922912	1111447
Paired Optical Duplicate Reads	75624	65676	89379
% Duplicate Reads	11.9436	11.135100000000001	12.0803

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	15662340	14730874	16178150
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	15662340	14730874	16178150
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	15662340	14730874	16178150
Paired Reads (QC-failed)	0	0	0
Read1	7831170	7365437	8089075
Read1 (QC-failed)	0	0	0
Read2	7831170	7365437	8089075
Read2 (QC-failed)	0	0	0
Properly Paired Reads	15662340	14730874	16178150
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	15662340	14730874	16178150
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	8857117	8229145	9148496
Distinct Fragments	7802170	7333126	8045942
Positions with Two Read	861975	742844	908302
NRF = Distinct/Total	0.880893	0.891116	0.879482
PBC1 = OneRead/Distinct	0.877837	0.88884	0.875627
PBC2 = OneRead/TwoRead	7.945741	8.774355	7.756498

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	71760	1313
N1	49238	464
N2	42437	756
Np	71449	1559
N optimal	71760	1559
N conservative	71760	1313
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.004352755112038	1.1873571972581873
Self Consistency Ratio	1.1602610929142023	1.6293103448275863
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	114638	117057

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	62.0	76.0	76.0
25 percentile	290.0	250.0	304.0	304.0
50 percentile (median)	290.0	250.0	304.0	304.0
75 percentile	290.0	250.0	304.0	304.0
Max size	290.0	426.0	454.0	454.0
Mean	289.88829184040196	249.84497296189036	287.0513149454779	303.6271181716834

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	8407325	7985110
Estimated Fragment Length	150	130
Cross-correlation at Estimated Fragment Length	0.725452528449546	0.718991290602942
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7256016	0.718841
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7205205	0.7131302
NSC (Normalized Strand Cross-correlation coeff.)	1.006845	1.008219
RSC (Relative Strand Cross-correlation coeff.)	0.970668	1.026321

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	0.4119499321661083	0.40751243666546133
Synthetic AUC	0.49838427677661024	0.4983050394216101
X-intercept	0.018517076482274603	0.018758673016063175
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5097886529495742	0.5269240368584464
Synthetic Elbow Point	0.49843588773388525	0.4998537576894954
JS Distance	0.03602538375499047	0.04409787062873255
Synthetic JS Distance	0.13205519251295017	0.14193303202566726
% Genome Enriched	41.38708357043737	40.416504437589225
Diff. Enrichment	8.97402445066698	9.547642006725354
CHANCE Divergence	0.0762987216367227	0.08122490322120339

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	0.4976082117997694	0.47358574922302643	0.4610422197449423	0.4207548824659172	0.4457137311538378	0.4045550052977176	0.4635026423990566	0.4846591423559784	0.48588342686518293

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	0.33608097518084135	0.2488354869068096	0.20452914063347497	0.3351920596485781

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	0.012916073963089261	0.005688166646873966	0.013382369572911968	0.014591250533754015

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