QC Report

	general
Report generated at	2022-12-26 16:31:12
Title	R02D3.7_OP218_L4larva_1_1
Description	ENCSR588GIM
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	1188773	1036054	1010306	3316166
Paired Reads	0	0	0	0
Unmapped Reads	0	0	0	0
Unpaired Duplicate Reads	68762	40480	62678	189134
Paired Duplicate Reads	0	0	0	0
Paired Optical Duplicate Reads	0	0	0	0
% Duplicate Reads	5.7843	3.9071000000000002	6.2039	5.7034

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	1120011	995574	947628	3127032
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	1120011	995574	947628	3127032
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	1170307	1025050	995541	3288896
Distinct Fragments	1108898	987822	937776	3112596
Positions with Two Read	51345	31690	49519	141053
NRF = Distinct/Total	0.947527	0.963682	0.941976	0.946395
PBC1 = OneRead/Distinct	0.949954	0.965682	0.943328	0.949734
PBC2 = OneRead/TwoRead	20.516155	30.101672	17.864456	20.95764

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	4600	324
N1	5918	316
N2	5452	207
N3	4330	245
Np	4816	351
N optimal	4816	351
N conservative	4600	324
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep3
Rescue Ratio	1.0469565217391303	1.0833333333333333
Self Consistency Ratio	1.366743648960739	1.5265700483091786
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	rep3
Number of peaks	20534	22289	23694

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	159.0	172.0	152.0	155.0	155.0
25 percentile	636.0	690.0	610.0	351.5	620.0
50 percentile (median)	636.0	690.0	610.0	587.0	620.0
75 percentile	636.0	690.0	610.0	620.0	620.0
Max size	807.0	731.0	610.0	974.0	974.0
Mean	634.02912243109	689.0611063753421	608.9045327931121	507.34472934472933	611.0830564784053

Enrichment / Signal-to-noise ratio

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

	rep1	rep2	rep3
Number of Subsampled Reads	1170307	1025050	995541
Estimated Fragment Length	125	130	165
Cross-correlation at Estimated Fragment Length	0.327949562522753	0.299557191456817	0.288574155255433
Phantom Peak	35	35	40
Cross-correlation at Phantom Peak	0.3246523	0.2991767	0.2839599
Argmin of Cross-correlation	1500	1500	1500
Minimum of Cross-correlation	0.299528	0.2820385	0.2669286
NSC (Normalized Strand Cross-correlation coeff.)	1.094888	1.062115	1.081091
RSC (Relative Strand Cross-correlation coeff.)	1.131236	1.022202	1.270931

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	0.31562362077919087	0.3198706754842162	0.31778831590590406
Synthetic AUC	0.48940662461639894	0.48876010742016424	0.48847932917843745
X-intercept	0.0592968954160358	0.0634960531906617	0.06531934545004797
Synthetic X-intercept	1.5226980044189402e-75	5.4889733830504754e-67	1.0286705988553223e-63
Elbow Point	0.5732139615512746	0.526157461434576	0.5465587852165709
Synthetic Elbow Point	0.5062593827167615	0.500944253568202	0.5199971683931245
JS Distance	0.12595611632983597	0.10695825348197972	0.11215704511727549
Synthetic JS Distance	0.23754339190925827	0.22232265218099062	0.22571087508206053
% Genome Enriched	32.61718243495295	36.69704822149211	34.50411038698081
Diff. Enrichment	19.462548488643293	19.38500242003115	19.455108215797566
CHANCE Divergence	0.16604791943872652	0.16525007418151225	0.16577888626827333

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	0.22457993716133146	0.22977699297088916	0.23541305237920365	0.24818841226701144	0.22922253895742556	0.21512238979852855	0.25117097168775276	0.23913842667647006	0.2260254023730831	0.1252590009248459	0.1820205836092418	0.17974792472737766

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	0.07304585087618784	0.07365664744828387	0.07083216217742612	0.09543656267661657	0.07885199894734093	0.06768689823432823	0.07466669800630907

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	0.021896616395921536	0.023485470974431096	0.021753629277493927	0.027561336451159855	0.017797772943045923	0.020967088351125124	0.02415992619514216

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