QC Report

	general
Report generated at	2022-12-19 19:38:50
Title	egl-27_OP177_L1larva_1_1
Description	ENCSR180AQI
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	491475	1870794	1369400	5097986
Paired Reads	0	0	0	0
Unmapped Reads	0	0	0	0
Unpaired Duplicate Reads	50742	246522	89074	374332
Paired Duplicate Reads	0	0	0	0
Paired Optical Duplicate Reads	0	0	0	0
% Duplicate Reads	10.3244	13.1774	6.504600000000001	7.342700000000001

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	440733	1624272	1280326	4723654
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	440733	1624272	1280326	4723654
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	480012	1804504	1353440	4966008
Distinct Fragments	432562	1602118	1270047	4699310
Positions with Two Read	40143	166233	71700	204429
NRF = Distinct/Total	0.901148	0.887844	0.938384	0.946295
PBC1 = OneRead/Distinct	0.899106	0.885747	0.939446	0.951974
PBC2 = OneRead/TwoRead	9.688339	8.536644	16.640739	21.883485

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	6092	338
N1	1055	79
N2	7054	110
N3	5798	438
Np	5781	505
N optimal	6092	505
N conservative	6092	338
Optimal Set	rep2_vs_rep3	pooled-pr1_vs_pooled-pr2
Conservative Set	rep2_vs_rep3	rep1_vs_rep3
Rescue Ratio	1.053796920947933	1.4940828402366864
Self Consistency Ratio	6.6862559241706165	5.544303797468355
Reproducibility Test	borderline	borderline

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	14947	24403	31815

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	137.0	307.0	134.0	126.0	126.0
25 percentile	504.0	550.0	470.0	504.0	504.0
50 percentile (median)	504.0	550.0	470.0	504.0	504.0
75 percentile	504.0	550.0	470.0	504.0	504.0
Max size	548.0	5218.0	470.0	2784.0	2784.0
Mean	503.75058540175286	553.6663524976437	469.8815967311017	515.6712871287128	504.94172685489167

Enrichment / Signal-to-noise ratio

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

	rep1	rep2	rep3
Number of Subsampled Reads	480012	1804504	1353440
Estimated Fragment Length	125	170	125
Cross-correlation at Estimated Fragment Length	0.151057835364996	0.379226743892882	0.346681020463918
Phantom Peak	30	35	40
Cross-correlation at Phantom Peak	0.1489835	0.3783168	0.3424401
Argmin of Cross-correlation	1500	1500	1500
Minimum of Cross-correlation	0.1408361	0.3702117	0.3283551
NSC (Normalized Strand Cross-correlation coeff.)	1.072579	1.024351	1.055811
RSC (Relative Strand Cross-correlation coeff.)	1.254597	1.112262	1.301091

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	0.26448062572375736	0.3456761269939071	0.317092460201306
Synthetic AUC	0.48308986273516097	0.49120720527488	0.49009279683541646
X-intercept	0.17736758424915366	0.048252377409077944	0.061253069635593606
Synthetic X-intercept	3.781863340177096e-29	3.627617384347604e-110	1.6004102863065918e-86
Elbow Point	0.633808183434042	0.5522451479310008	0.5659081433367712
Synthetic Elbow Point	0.4982649828043226	0.5028803657560705	0.4943189142336573
JS Distance	0.14628806827259108	0.06817609512811215	0.10606402052673584
Synthetic JS Distance	0.23738776610427012	0.19964145642718628	0.23062905553278074
% Genome Enriched	35.66482671395884	38.819344838523705	36.599831232382634
Diff. Enrichment	27.601772086423487	13.736720107312934	16.912408559404383
CHANCE Divergence	0.23742863822155597	0.11703272703009814	0.1442543149681829

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	0.19396777640884616	0.21449055330634278	0.27545718824736826	0.12337600457418761	0.2570394613710019	0.23623670846331324	0.1584454952215859	0.262204852389255	0.23255483369079438	0.14794679510039516	0.1958274993333995	0.20027680378318433

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	0.053096988011051824	0.060924912960780266	0.07898202001535871	0.03407278329510157	0.08104984879379808	0.08342797068871521	0.07760069182989665

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	0.015277710935031542	0.02044521155006784	0.018905453600854445	0.013817889742769433	0.01613953820542372	0.020386214136087214	0.023948601797550078

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