QC Report

	general
Report generated at	2021-08-30 19:50:40
Title	mab-9_RW12257_L1larva_2_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	18457502	13354888	13110036
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	17831960	12771459	12442987
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	96.6	95.6	94.89999999999999
Paired Reads	18457502	13354888	13110036
Paired Reads (QC-failed)	0	0	0
Read1	9228751	6677444	6555018
Read1 (QC-failed)	0	0	0
Read2	9228751	6677444	6555018
Read2 (QC-failed)	0	0	0
Properly Paired Reads	17739564	12700372	12285150
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	96.1	95.1	93.7
With itself	17821446	12762722	12432948
With itself (QC-failed)	0	0	0
Singletons	10514	8737	10039
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	6171	5833	10971
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	8175379	5864672	5700610
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1129158	776737	776335
Paired Optical Duplicate Reads	51522	37793	38874
% Duplicate Reads	13.811699999999998	13.2443	13.618500000000001

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	14092442	10175870	9848550
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14092442	10175870	9848550
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	14092442	10175870	9848550
Paired Reads (QC-failed)	0	0	0
Read1	7046221	5087935	4924275
Read1 (QC-failed)	0	0	0
Read2	7046221	5087935	4924275
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14092442	10175870	9848550
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	14092442	10175870	9848550
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	8134875	5831632	5551239
Distinct Fragments	7013098	5060444	4801214
Positions with Two Read	865988	603307	581643
NRF = Distinct/Total	0.862103	0.867758	0.864891
PBC1 = OneRead/Distinct	0.859462	0.865222	0.862439
PBC2 = OneRead/TwoRead	6.960248	7.257347	7.119063

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	95641	1431
N1	81265	824
N2	58359	869
Np	97612	1492
N optimal	97612	1492
N conservative	95641	1431
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.020608316516975	1.0426275331935708
Self Consistency Ratio	1.3925015850168783	1.0546116504854368
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	148458	136741

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	71.0	75.0	80.0	80.0
25 percentile	284.0	300.0	320.0	320.0
50 percentile (median)	284.0	300.0	320.0	320.0
75 percentile	284.0	300.0	320.0	320.0
Max size	284.0	302.0	320.0	320.0
Mean	283.92864648587476	299.89182469047324	304.5402144772118	319.7630926525427

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7711631	5530240
Estimated Fragment Length	160	165
Cross-correlation at Estimated Fragment Length	0.70022036349683	0.629186773466086
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7000426	0.6287382
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6953901	0.6239444
NSC (Normalized Strand Cross-correlation coeff.)	1.006946	1.008402
RSC (Relative Strand Cross-correlation coeff.)	1.038214	1.093578

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	0.41438798847837643	0.4071149706236783
Synthetic AUC	0.49830467811221885	0.4980075396228268
X-intercept	0.01900170674012636	0.019502749747981357
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5309838209020771	0.5390084937768862
Synthetic Elbow Point	0.5014809684321475	0.4988591339568133
JS Distance	0.07825486753599689	0.0762172850574312
Synthetic JS Distance	0.13200391441054252	0.14099077993471873
% Genome Enriched	49.92703935483227	48.23427253944965
Diff. Enrichment	4.961081829768172	6.141974034307779
CHANCE Divergence	0.042807302618339836	0.05278166086465227

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	0.5984608629221252	0.5910359507344335	0.5819236180750479	0.5480291025673278	0.5814527505527787	0.5307458783860011	0.6042936154768408	0.595888400332351	0.5967966946851012

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	0.43290324436244265	0.3627499761929125	0.2943426950226369	0.4413957180046144

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	0.01779266724442969	0.011463023938647397	0.013657014093143878	0.018194096070629058

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