QC Report

	general
Report generated at	2022-03-18 12:46:28
Title	dmd-9_RJP5357_L4larva_1_1
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	14615820	17904986	12864966
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14467627	17539718	12749458
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.0	98.0	99.1
Paired Reads	14615820	17904986	12864966
Paired Reads (QC-failed)	0	0	0
Read1	7307910	8952493	6432483
Read1 (QC-failed)	0	0	0
Read2	7307910	8952493	6432483
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14414704	17476206	12684448
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.6	97.6	98.6
With itself	14457062	17526084	12738920
With itself (QC-failed)	0	0	0
Singletons	10565	13634	10538
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	4570	5219	11230
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	6625708	8036157	5847026
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	953808	1540333	766660
Paired Optical Duplicate Reads	48822	77545	48472
% Duplicate Reads	14.3956	19.1675	13.111999999999998

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	11343800	12991648	10160732
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	11343800	12991648	10160732
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	11343800	12991648	10160732
Paired Reads (QC-failed)	0	0	0
Read1	5671900	6495824	5080366
Read1 (QC-failed)	0	0	0
Read2	5671900	6495824	5080366
Read2 (QC-failed)	0	0	0
Properly Paired Reads	11343800	12991648	10160732
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	11343800	12991648	10160732
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	6551154	7922099	5749376
Distinct Fragments	5613903	6410632	4999249
Positions with Two Read	724452	1056178	603265
NRF = Distinct/Total	0.856933	0.809209	0.869529
PBC1 = OneRead/Distinct	0.853185	0.802704	0.865394
PBC2 = OneRead/TwoRead	6.611476	4.872135	7.171505

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	85524	1346
N1	38539	569
N2	40616	545
Np	85877	1379
N optimal	85877	1379
N conservative	85524	1346
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0041274963752864	1.0245170876671619
Self Consistency Ratio	1.053893458574431	1.0440366972477064
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	135841	132668

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	65.0	68.0	71.0	71.0
25 percentile	260.0	270.0	284.0	284.0
50 percentile (median)	260.0	270.0	284.0	284.0
75 percentile	260.0	270.0	284.0	284.0
Max size	260.0	270.0	284.0	284.0
Mean	259.9651651563225	269.9563798353785	276.31036983321246	283.87652107083386

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	6177113	7467328
Estimated Fragment Length	160	160
Cross-correlation at Estimated Fragment Length	0.652738864848227	0.67634316371765
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6526002	0.6759766
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6484491	0.671886
NSC (Normalized Strand Cross-correlation coeff.)	1.006615	1.006634
RSC (Relative Strand Cross-correlation coeff.)	1.033395	1.089616

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	0.4076427579619252	0.4087549747514834
Synthetic AUC	0.49810701538402335	0.498232251349251
X-intercept	0.018924976698048625	0.01882917424271153
Synthetic X-intercept	0.0	0.0
Elbow Point	0.533370190666845	0.5369108897453451
Synthetic Elbow Point	0.5026247824231473	0.5020684797208385
JS Distance	0.03431163997782106	0.027065327451210475
Synthetic JS Distance	0.14524378206659805	0.14754906419859642
% Genome Enriched	43.899479273737555	43.207306533927046
Diff. Enrichment	8.70118539949996	8.585835236116319
CHANCE Divergence	0.07399766889780242	0.0729806024592456

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	0.5482060685131966	0.5407433298685432	0.4146841446428886	0.42057712770543043	0.4182212309808001	0.40358374857446877	0.5345627086873437	0.5439982859571766	0.5426251450147949

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	0.3724054309581644	0.18904123838572612	0.2000776960705832	0.3735759045816621

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	0.013068877959427745	0.007081665755743225	0.006697610649549619	0.01336601652042732

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