QC Report

	general
Report generated at	2022-12-26 15:51:22
Title	T23F11.4_OP709_lateembryonic_1_1
Description	ENCSR434ALY
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	11168680	20255899	13945802
Paired Reads	0	0	0
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	1041526	2583656	1403065
Paired Duplicate Reads	0	0	0
Paired Optical Duplicate Reads	0	0	0
% Duplicate Reads	9.3254	12.7551	10.0608

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	10127154	17672243	12542737
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	10127154	17672243	12542737
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	11125729	20177801	13889639
Distinct Fragments	10110073	17655203	12523075
Positions with Two Read	803852	1911219	1081129
NRF = Distinct/Total	0.908711	0.874982	0.901613
PBC1 = OneRead/Distinct	0.911826	0.877252	0.903864
PBC2 = OneRead/TwoRead	11.46807	8.103763	10.469758

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	11157	545
N1	11050	226
N2	9787	280
Np	11456	460
N optimal	11456	545
N conservative	11157	545
Optimal Set	pooled-pr1_vs_pooled-pr2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.026799318813301	1.184782608695652
Self Consistency Ratio	1.1290487381219985	1.238938053097345
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
Number of peaks	25609	20918

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	155.0	151.0	151.0	151.0
25 percentile	620.0	604.0	604.0	604.0
50 percentile (median)	620.0	604.0	604.0	604.0
75 percentile	620.0	604.0	604.0	604.0
Max size	620.0	604.0	604.0	604.0
Mean	619.6655863173103	603.6571373936323	575.3266055045872	602.6359113128492

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	11125729	15000000
Estimated Fragment Length	175	200
Cross-correlation at Estimated Fragment Length	0.795368975318919	0.840449118078292
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.795513	0.8406368
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7908631	0.8360476
NSC (Normalized Strand Cross-correlation coeff.)	1.005697	1.005265
RSC (Relative Strand Cross-correlation coeff.)	0.9690174	0.95911

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	0.40383388628003347	0.4117864516614793
Synthetic AUC	0.4971839675492207	0.49786825362597814
X-intercept	0.0290173980587177	0.02857810356567353
Synthetic X-intercept	0.0	0.0
Elbow Point	0.45616939195651784	0.4288073354193166
Synthetic Elbow Point	0.49828554775270967	0.5038808200771392
JS Distance	0.035569546150630245	0.024795426094364248
Synthetic JS Distance	0.14031525673411283	0.1336214960775633
% Genome Enriched	40.18945573409105	38.95344077411677
Diff. Enrichment	6.71262578724482	5.259703381701231
CHANCE Divergence	0.05704072312029162	0.044748646902736375

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	0.1960661405958673	0.15726413449611348	0.22026010466514087	0.1854293093735012	0.23064426590135786	0.19063297118724382	0.16854124569680415	0.1866263434913231	0.17816559755470945

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	0.08546160191891931	0.08948298801420419	0.07599273052096443	0.0879074103657716

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	0.007145406787060885	0.004493957532392615	0.004105251382068479	0.006188911219908835

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