QC Report

	general
Report generated at	2022-12-19 19:37:48
Title	egl-27_OP177_L4larva_2_1
Description	ENCSR206TOT
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	291006	601350	220292	660616
Paired Reads	0	0	0	0
Unmapped Reads	0	0	0	0
Unpaired Duplicate Reads	9005	35516	4338	17086
Paired Duplicate Reads	0	0	0	0
Paired Optical Duplicate Reads	0	0	0	0
% Duplicate Reads	3.0944	5.906000000000001	1.9692	2.5864000000000003

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	282001	565834	215954	643530
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	282001	565834	215954	643530
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	282722	576326	216158	636122
Distinct Fragments	275235	550733	212284	630444
Positions with Two Read	6987	23539	2926	5219
NRF = Distinct/Total	0.973518	0.955593	0.982078	0.991074
PBC1 = OneRead/Distinct	0.973728	0.955563	0.984167	0.991374
PBC2 = OneRead/TwoRead	38.357521	22.35694	71.402256	119.755892

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	3145	44
N1	762	31
N2	2037	42
N3	288	288
Np	5986	78
N optimal	5986	78
N conservative	3145	44
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.9033386327503974	1.7727272727272727
Self Consistency Ratio	7.072916666666667	9.290322580645162
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	12952	11540	7790

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	730.0	616.0	580.0	716.0	716.0
25 percentile	730.0	616.0	580.0	716.0	716.0
50 percentile (median)	730.0	616.0	580.0	716.0	716.0
75 percentile	730.0	616.0	580.0	716.0	716.0
Max size	730.0	616.0	580.0	716.0	716.0
Mean	730.0	616.0	580.0	716.0	716.0

Enrichment / Signal-to-noise ratio

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

	rep1	rep2	rep3
Number of Subsampled Reads	282722	576326	216158
Estimated Fragment Length	150	115	125
Cross-correlation at Estimated Fragment Length	0.103845454475653	0.183899920015075	0.0821184974083244
Phantom Peak	30	30	30
Cross-correlation at Phantom Peak	0.1036581	0.1846144	0.08188801
Argmin of Cross-correlation	1500	1500	1500
Minimum of Cross-correlation	0.09966294	0.178282	0.07813312
NSC (Normalized Strand Cross-correlation coeff.)	1.041967	1.031511	1.051008
RSC (Relative Strand Cross-correlation coeff.)	1.046905	0.8871644	1.061383

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	0.2393888010675035	0.2888984411108224	0.20822689447442613
Synthetic AUC	0.47885103617737407	0.4850842946401125	0.4758450703944352
X-intercept	0.2854439026335996	0.12017630458411863	0.3826667065545816
Synthetic X-intercept	1.934743763959526e-18	1.150702587183179e-37	4.826277118737434e-14
Elbow Point	0.6095112733219653	0.5283792542954299	0.7089299069614383
Synthetic Elbow Point	0.503615188158551	0.504451328434004	0.5301676646880601
JS Distance	0.08789557931239579	0.05444575288000329	0.10702293895336144
Synthetic JS Distance	0.21257029119963702	0.23604240917904848	0.20343014607423662
% Genome Enriched	38.50619758478675	40.33106969415941	31.091233633489892
Diff. Enrichment	31.825316509847102	22.120318318229256	35.94640170681349
CHANCE Divergence	0.2807455579101107	0.19166859009888398	0.31068259280303895

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	0.1883929489611739	0.14898185686968263	0.1324078275929133	0.1531833107566613	0.16486107232863348	0.09068597942154348	0.1371063829787234	0.1979308419076973	0.06916287727942062	0.4235454587328878	0.19824777446676506	0.2042737838742306

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	0.05506167106446861	0.025778608351844208	0.02995048830172149	0.02763465377782348	0.04836224051576964	0.009432564342406254	0.0787693800180299

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	0.02066105214473923	0.0001513458025980716	0.0014673962599726074	0.01869142308006	0.02316227020645631	0.009576113431564129	0.02166783074463075

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