QC Report

	general
Report generated at	2021-08-28 15:16:06
Title	ctbp-1_RW12203_L4larva_1_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	13003824	11835020	12142472
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	11769633	10760230	12007422
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	90.5	90.9	98.9
Paired Reads	13003824	11835020	12142472
Paired Reads (QC-failed)	0	0	0
Read1	6501912	5917510	6071236
Read1 (QC-failed)	0	0	0
Read2	6501912	5917510	6071236
Read2 (QC-failed)	0	0	0
Properly Paired Reads	11678598	10718532	11901384
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	89.8	90.60000000000001	98.0
With itself	11757968	10751922	11997908
With itself (QC-failed)	0	0	0
Singletons	11665	8308	9514
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	3673	2842	39349
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	5358492	4919184	5451202
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	731211	641801	768748
Paired Optical Duplicate Reads	30150	28125	37077
% Duplicate Reads	13.6458	13.0469	14.102400000000001

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	9254562	8554766	9364908
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	9254562	8554766	9364908
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	9254562	8554766	9364908
Paired Reads (QC-failed)	0	0	0
Read1	4627281	4277383	4682454
Read1 (QC-failed)	0	0	0
Read2	4627281	4277383	4682454
Read2 (QC-failed)	0	0	0
Properly Paired Reads	9254562	8554766	9364908
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	9254562	8554766	9364908
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	5256273	4822840	5348967
Distinct Fragments	4543094	4197914	4599748
Positions with Two Read	557285	498637	586697
NRF = Distinct/Total	0.864319	0.870424	0.859932
PBC1 = OneRead/Distinct	0.861201	0.867006	0.855799
PBC2 = OneRead/TwoRead	7.020677	7.299133	6.709531

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	54971	2775
N1	26729	1404
N2	27646	1715
Np	62620	2927
N optimal	62620	2927
N conservative	54971	2775
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.13914609521384	1.0547747747747749
Self Consistency Ratio	1.0343073066706574	1.2215099715099715
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	82456	98757

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	81.0	82.0	91.0	91.0
25 percentile	324.0	330.0	364.0	364.0
50 percentile (median)	324.0	330.0	364.0	364.0
75 percentile	324.0	330.0	364.0	364.0
Max size	449.0	425.0	554.0	554.0
Mean	323.77381876394685	329.72653077756513	346.4260334813803	363.18361545832005

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	4974291	4546846
Estimated Fragment Length	185	170
Cross-correlation at Estimated Fragment Length	0.604537649698317	0.586222658159604
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6038131	0.5850174
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.5977466	0.5788599
NSC (Normalized Strand Cross-correlation coeff.)	1.011361	1.012719
RSC (Relative Strand Cross-correlation coeff.)	1.119432	1.195733

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	0.3861432279560539	0.3799676688310617
Synthetic AUC	0.4978977143382709	0.4978154657471613
X-intercept	0.01963405630823872	0.019779715465810005
Synthetic X-intercept	0.0	0.0
Elbow Point	0.586375880439771	0.5961949039248159
Synthetic Elbow Point	0.5032747315515886	0.49970774463761813
JS Distance	0.06684315859640517	0.07708864392573073
Synthetic JS Distance	0.18107743316637162	0.1891819844309857
% Genome Enriched	38.94446994033961	38.28740746652832
Diff. Enrichment	11.956496224028024	12.867076046397285
CHANCE Divergence	0.10174922146342921	0.10953979176476046

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	0.4355437891063888	0.4992717509748367	0.3694611653234015	0.3917062391405588	0.3766510779550838	0.384345611404359	0.4866823161435401	0.5031072473689636	0.5031055642538707

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	0.3255173917847995	0.18570052261792616	0.19961036923745196	0.35784264291162476

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	0.04570430731580664	0.03024832509631466	0.03603839076369827	0.04759837092112628

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