QC Report

	general
Report generated at	2022-12-27 12:21:42
Title	ceh-9_OP202_L3larva_1_1
Description	ENCSR755UCK
Pipeline version	v1.3.6
Pipeline type	tf
Genome	WS245chr
Aligner	bwa
Sequencing endedness	{'rep1': {'paired_end': False}, 'rep2': {'paired_end': False}, 'ctl1': {'paired_end': False}}
Peak caller	spp

Alignment quality metrics

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	1742645	1732004	1702414
Paired Reads	0	0	0
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	534154	48546	33185
Paired Duplicate Reads	0	0	0
Paired Optical Duplicate Reads	0	0	0
% Duplicate Reads	30.651899999999998	2.8028999999999997	1.9493

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	1208491	1683458	1669229
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	1208491	1683458	1669229
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	0	0	0
Paired Reads (QC-failed)	0	0	0
Read1	0	0	0
Read1 (QC-failed)	0	0	0
Read2	0	0	0
Read2 (QC-failed)	0	0	0
Properly Paired Reads	0	0	0
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	0.0	0.0	0.0
With itself	0	0	0
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	1735909	1730314	1695987
Distinct Fragments	1204757	1681988	1664086
Positions with Two Read	290253	35192	22510
NRF = Distinct/Total	0.694021	0.972071	0.98119
PBC1 = OneRead/Distinct	0.672684	0.976559	0.984984
PBC2 = OneRead/TwoRead	2.792119	46.674273	72.816437

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	14409	14
N1	6124	31
N2	9989	1
Np	13688	13
N optimal	14409	14
N conservative	14409	14
Optimal Set	rep1_vs_rep2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0526738749269433	1.0769230769230769
Self Consistency Ratio	1.6311234487263226	31.0
Reproducibility Test	pass	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
Number of peaks	34644	31659

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	484.0	564.0	596.0	596.0
25 percentile	484.0	564.0	596.0	596.0
50 percentile (median)	484.0	564.0	596.0	596.0
75 percentile	484.0	564.0	596.0	596.0
Max size	484.0	564.0	596.0	596.0
Mean	484.0	564.0	596.0	596.0

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	1735909	1730314
Estimated Fragment Length	120	185
Cross-correlation at Estimated Fragment Length	0.295962640941567	0.404714586249028
Phantom Peak	30	30
Cross-correlation at Phantom Peak	0.290888	0.4026651
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.2820034	0.3961693
NSC (Normalized Strand Cross-correlation coeff.)	1.0495	1.02157
RSC (Relative Strand Cross-correlation coeff.)	1.571175	1.315515

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	0.33893158244313115	0.34361252989142166
Synthetic AUC	0.4897981998235167	0.4913592853172167
X-intercept	0.054509189911541495	0.048449732231009346
Synthetic X-intercept	1.537975508685061e-81	4.082042919489266e-114
Elbow Point	0.5019975466975157	0.5205887925962124
Synthetic Elbow Point	0.5094745847386982	0.49972766219700704
JS Distance	0.029375041110249366	0.02507124390943291
Synthetic JS Distance	0.19509894455583301	0.19579902611136837
% Genome Enriched	40.779073130354135	38.78451826513618
Diff. Enrichment	15.058463819551509	11.601128457085236
CHANCE Divergence	0.12896814992016284	0.09904488310624279

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	0.2530114001676471	0.2414779578700508	0.23315007463847506	0.2734894485042098	0.23037509619442445	0.2790981420385896	0.47141149446273084	0.24850014695966388	0.21959039374151956

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	0.10332443621931092	0.05377615555266858	0.07881158900311146	0.09484365042398742

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	0.0003174329837766849	0.002209366888127425	1.4850385337798745e-05	0.0003378344500542714

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