QC Report

	general
Report generated at	2022-12-19 19:26:40
Title	lin-15B_OP184_L4larva_1_1
Description	ENCSR205ZNH
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	1037204	1729570	946443	3341896
Paired Reads	0	0	0	0
Unmapped Reads	0	0	0	0
Unpaired Duplicate Reads	69882	89422	61136	181607
Paired Duplicate Reads	0	0	0	0
Paired Optical Duplicate Reads	0	0	0	0
% Duplicate Reads	6.737500000000001	5.1701999999999995	6.4596	5.4343

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	967322	1640148	885307	3160289
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	967322	1640148	885307	3160289
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	1026146	1716035	931712	3306738
Distinct Fragments	959405	1630752	875300	3143467
Positions with Two Read	57689	73238	47205	130751
NRF = Distinct/Total	0.93496	0.950302	0.939453	0.950625
PBC1 = OneRead/Distinct	0.93553	0.951978	0.941607	0.9539
PBC2 = OneRead/TwoRead	15.55846	21.197193	17.459782	22.933316

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	2562	136
N1	5181	76
N2	7356	83
N3	4369	130
Np	2282	181
N optimal	2562	181
N conservative	2562	136
Optimal Set	rep2_vs_rep3	pooled-pr1_vs_pooled-pr2
Conservative Set	rep2_vs_rep3	rep1_vs_rep3
Rescue Ratio	1.1226993865030674	1.3308823529411764
Self Consistency Ratio	1.6836804760814832	1.7105263157894737
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	23169	23175	21089

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	266.0	170.0	174.0	109.0	109.0
25 percentile	810.0	680.0	696.0	436.0	436.0
50 percentile (median)	810.0	680.0	696.0	436.0	436.0
75 percentile	810.0	680.0	696.0	436.0	436.0
Max size	810.0	680.0	696.0	436.0	436.0
Mean	809.78078466917	679.7534412081985	695.2830859689885	384.3867403314917	432.05542544886805

Enrichment / Signal-to-noise ratio

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

	rep1	rep2	rep3
Number of Subsampled Reads	1026146	1716035	931712
Estimated Fragment Length	135	105	100
Cross-correlation at Estimated Fragment Length	0.282496544229595	0.395941751350523	0.275723705259189
Phantom Peak	35	30	35
Cross-correlation at Phantom Peak	0.2820502	0.3957085	0.2739623
Argmin of Cross-correlation	1500	1500	1500
Minimum of Cross-correlation	0.2710874	0.3861096	0.2579196
NSC (Normalized Strand Cross-correlation coeff.)	1.042087	1.025465	1.06903
RSC (Relative Strand Cross-correlation coeff.)	1.040715	1.0243	1.109797

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	0.3315779017023417	0.35809199264193897	0.3181895385744325
Synthetic AUC	0.48859854341408065	0.4912489853669829	0.48806899186066927
X-intercept	0.06308586931585825	0.04717077111822616	0.06959115074259153
Synthetic X-intercept	4.505480305481592e-65	3.131834716966643e-111	2.4250333421077908e-59
Elbow Point	0.5114396002274155	0.5229420389598731	0.563637451749005
Synthetic Elbow Point	0.515005027084349	0.5162416500604342	0.49163140336114475
JS Distance	0.07775087715697312	0.04102270703050951	0.10283797602970775
Synthetic JS Distance	0.2003870909222154	0.1770467319780138	0.21860202130791498
% Genome Enriched	37.720657909173426	41.27312806088353	40.40256540690426
Diff. Enrichment	16.89715141701332	12.459478627239784	19.729826925333043
CHANCE Divergence	0.14401977677028532	0.10636247681992121	0.1692993030404649

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	0.23310128375039543	0.19727853827825295	0.21829489657260137	0.2317366916083786	0.2522308962361933	0.20645922097168443	0.23351066139300047	0.2502444901313784	0.2182341472891859	0.061633193301490474	0.14055402318727386	0.14240478061003625

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	0.02668621558146999	0.027382223371260176	0.028948026169434808	0.06406243215806112	0.06916692883812924	0.06431328341467987	0.027917900283928807

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	0.0068255144831748495	0.008185177582193195	0.006209099521670007	0.009318510278893688	0.005069664444915947	0.011532722547093833	0.008680771775581436

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