QC Report

	general
Report generated at	2021-08-31 18:49:49
Title	pop-1_JIM531_earlyembryonic_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	17187514	14852696	12997252
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	17025823	14729972	12966192
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.1	99.2	99.8
Paired Reads	17187514	14852696	12997252
Paired Reads (QC-failed)	0	0	0
Read1	8593757	7426348	6498626
Read1 (QC-failed)	0	0	0
Read2	8593757	7426348	6498626
Read2 (QC-failed)	0	0	0
Properly Paired Reads	16658774	14285082	12671330
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	96.89999999999999	96.2	97.5
With itself	17007460	14711914	12949088
With itself (QC-failed)	0	0	0
Singletons	18363	18058	17104
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	10933	10292	102755
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	7493734	6404004	5579510
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1243460	977759	757850
Paired Optical Duplicate Reads	92437	78143	67873
% Duplicate Reads	16.5933	15.267900000000001	13.5827

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	12500548	10852490	9643320
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	12500548	10852490	9643320
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	12500548	10852490	9643320
Paired Reads (QC-failed)	0	0	0
Read1	6250274	5426245	4821660
Read1 (QC-failed)	0	0	0
Read2	6250274	5426245	4821660
Read2 (QC-failed)	0	0	0
Properly Paired Reads	12500548	10852490	9643320
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	12500548	10852490	9643320
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	7405042	6337017	5561080
Distinct Fragments	6182311	5374332	4807209
Positions with Two Read	894763	724417	576379
NRF = Distinct/Total	0.834879	0.848085	0.864438
PBC1 = OneRead/Distinct	0.830737	0.844572	0.862914
PBC2 = OneRead/TwoRead	5.73993	6.265746	7.197014

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	67334	952
N1	61495	431
N2	59824	390
Np	67363	975
N optimal	67363	975
N conservative	67334	952
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0004306888050614	1.0241596638655461
Self Consistency Ratio	1.027931933672105	1.1051282051282052
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	90126	91350

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	78.0	78.0	85.0	85.0
25 percentile	304.0	310.0	340.0	340.0
50 percentile (median)	304.0	310.0	340.0	340.0
75 percentile	304.0	310.0	340.0	340.0
Max size	4684.0	2310.0	5722.0	5722.0
Mean	304.6131859840668	310.2925561029009	418.9979487179487	341.14932529727

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7114758	6150258
Estimated Fragment Length	175	160
Cross-correlation at Estimated Fragment Length	0.671869321901988	0.644413706283163
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.671566	0.6441583
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6662643	0.639226
NSC (Normalized Strand Cross-correlation coeff.)	1.008413	1.008116
RSC (Relative Strand Cross-correlation coeff.)	1.057209	1.051783

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	0.4039940476315353	0.4015016278776385
Synthetic AUC	0.49818886262566237	0.49805497624490735
X-intercept	0.01875837070835903	0.018742402740103352
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5452023241377796	0.5412861799230743
Synthetic Elbow Point	0.5030103686591155	0.49819518688415126
JS Distance	0.18117763690386005	0.17517831878944035
Synthetic JS Distance	0.1520245474784893	0.15290854410375868
% Genome Enriched	2.2237391792065115	2.46665189629603
Diff. Enrichment	1.7084907462741383	1.517300798653154
CHANCE Divergence	0.03244330602393398	0.02788015547051097

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	0.3447408865595332	0.35414646776914793	0.3760891122533188	0.3835677556822894	0.37396904519705854	0.38373265190433753	0.33052954395055584	0.3498172400681025	0.34789720702695787

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	0.2793327360662882	0.25561839368962064	0.25396835196346645	0.2793673782400388

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	0.021439180632515563	0.01846175063685208	0.016345649708039353	0.02156888538441979

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