QC Report

	general
Report generated at	2022-12-27 05:01:19
Title	attf-4_OP219_L4larva_1_1
Description	ENCSR678ZPU
Pipeline version	v1.3.6
Pipeline type	tf
Genome	WS245chr
Aligner	bwa
Sequencing endedness	{'rep1': {'paired_end': False}, 'rep2': {'paired_end': False}, 'rep3': {'paired_end': False}, 'ctl1': {'paired_end': False}}
Peak caller	spp

Alignment quality metrics

Marking duplicates (filtered BAM)

	rep1	rep2	rep3	ctl1
Unpaired Reads	1117114	665281	1676613	4309404
Paired Reads	0	0	0	0
Unmapped Reads	0	0	0	0
Unpaired Duplicate Reads	205303	30276	183533	187474
Paired Duplicate Reads	0	0	0	0
Paired Optical Duplicate Reads	0	0	0	0
% Duplicate Reads	18.378	4.5509	10.9467	4.3503

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	rep3	ctl1
Total Reads	911811	635005	1493080	4121930
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	911811	635005	1493080	4121930
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0
Paired Reads	0	0	0	0
Paired Reads (QC-failed)	0	0	0	0
Read1	0	0	0	0
Read1 (QC-failed)	0	0	0	0
Read2	0	0	0	0
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	0	0	0	0
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	0.0	0.0	0.0	0.0
With itself	0	0	0	0
With itself (QC-failed)	0	0	0	0
Singletons	0	0	0	0
Singletons (QC-failed)	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0
Diff. Chroms (QC-failed)	0	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	rep3	ctl1
Total Fragments	1092689	649668	1637475	4248344
Distinct Fragments	900081	625352	1477420	4102546
Positions with Two Read	137751	20193	122878	116594
NRF = Distinct/Total	0.82373	0.962572	0.902255	0.965681
PBC1 = OneRead/Distinct	0.819667	0.96524	0.907221	0.9691
PBC2 = OneRead/TwoRead	5.355801	29.892289	10.907949	34.099319

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	4477	56
N1	4346	35
N2	3066	27
N3	6236	42
Np	3772	72
N optimal	4477	72
N conservative	4477	56
Optimal Set	rep1_vs_rep3	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep3	rep1_vs_rep3
Rescue Ratio	1.1869034994697774	1.2857142857142858
Self Consistency Ratio	2.0339204174820615	1.5555555555555556
Reproducibility Test	borderline	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	rep3
Number of peaks	24453	22093	19756

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	rep3	idr_opt	overlap_opt
Min size	211.0	749.0	166.0	126.0	126.0
25 percentile	730.0	900.0	660.0	504.0	504.0
50 percentile (median)	730.0	900.0	660.0	504.0	504.0
75 percentile	730.0	900.0	660.0	504.0	504.0
Max size	1008.0	3135.0	683.0	3010.0	3010.0
Mean	729.8701590806854	900.850767211334	659.7397752581494	699.625	507.46258655349567

Enrichment / Signal-to-noise ratio

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

	rep1	rep2	rep3
Number of Subsampled Reads	1092689	649668	1637475
Estimated Fragment Length	115	135	110
Cross-correlation at Estimated Fragment Length	0.254687694051762	0.223344363319463	0.35840999887728
Phantom Peak	35	25	30
Cross-correlation at Phantom Peak	0.2542856	0.2231028	0.356248
Argmin of Cross-correlation	1500	1500	1500
Minimum of Cross-correlation	0.2440454	0.2066885	0.3515827
NSC (Normalized Strand Cross-correlation coeff.)	1.043608	1.080584	1.019419
RSC (Relative Strand Cross-correlation coeff.)	1.039267	1.014717	1.463423

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	rep3
AUC	0.32238263188042626	0.30072010591467685	0.3427500149905014
Synthetic AUC	0.48824678534009397	0.4859040548087286	0.4908236662917961
X-intercept	0.06860664142451893	0.10298277602448143	0.04959124477834655
Synthetic X-intercept	3.518527209940818e-61	2.878095080222016e-42	4.7410195073917643e-101
Elbow Point	0.5442449100100144	0.5999365621471519	0.5411986961326849
Synthetic Elbow Point	0.5162428903808125	0.5158318024868325	0.5049768129299167
JS Distance	0.09962294012404359	0.12190422514061897	0.0739627411226263
Synthetic JS Distance	0.21283300966322927	0.2220922872471032	0.19941593216650078
% Genome Enriched	41.150619017790525	38.270181416299934	36.73470609123081
Diff. Enrichment	18.27002236649877	22.150203586955808	14.809513144676888
CHANCE Divergence	0.15705753827914684	0.18999251510463674	0.12601684192214174

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for spp raw peaks

	rep1	rep2	rep3	rep1-pr1	rep2-pr1	rep3-pr1	rep1-pr2	rep2-pr2	rep3-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.23953209601551198	0.2522657301911009	0.1892269670747716	0.21569797282773204	0.2085964542067319	0.24114849840597957	0.21966637786380935	0.1751579517609338	0.24647975995927882	0.1376856313505462	0.1782408488705871	0.18020036224947317

FRiP for overlap peaks

	rep1_vs_rep2	rep1_vs_rep3	rep2_vs_rep3	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	rep3-pr1_vs_rep3-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.04404065139070547	0.05149880127478045	0.04929773913318087	0.05547092544397907	0.05116967582932418	0.06803453264393067	0.04507687105085174

FRiP for IDR peaks

	rep1_vs_rep2	rep1_vs_rep3	rep2_vs_rep3	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	rep3-pr1_vs_rep3-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.011292491585238443	0.012020805974941248	0.011189527536468354	0.009416425114415159	0.014059731813135329	0.006460470972754306	0.010560558650690681

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