QC Report


general
Report generated at2022-12-20 11:46:06
Titleceh-24_OP673_lateembryonic_1_1
DescriptionENCSR282OTW
Pipeline versionv1.3.6
Pipeline typetf
GenomeWS245chr
Alignerbwa
Sequencing endedness{'rep1': {'paired_end': False}, 'rep2': {'paired_end': False}, 'ctl1': {'paired_end': False}}
Peak callerspp

Alignment quality metrics


Marking duplicates (filtered BAM)

rep1rep2ctl1
Unpaired Reads169223651446932856284134
Paired Reads000
Unmapped Reads000
Unpaired Duplicate Reads2164883165476412378988
Paired Duplicate Reads000
Paired Optical Duplicate Reads000
% Duplicate Reads12.79311.43639999999999921.9937

Filtered out (samtools view -F 1804):


SAMstat (filtered/deduped BAM)

rep1rep2ctl1
Total Reads147574821281456443905146
Total Reads (QC-failed)000
Duplicate Reads000
Duplicate Reads (QC-failed)000
Mapped Reads147574821281456443905146
Mapped Reads (QC-failed)000
% Mapped Reads100.0100.0100.0
Paired Reads000
Paired Reads (QC-failed)000
Read1000
Read1 (QC-failed)000
Read2000
Read2 (QC-failed)000
Properly Paired Reads000
Properly Paired Reads (QC-failed)000
% Properly Paired Reads0.00.00.0
With itself000
With itself (QC-failed)000
Singletons000
Singletons (QC-failed)000
% Singleton0.00.00.0
Diff. Chroms000
Diff. Chroms (QC-failed)000

Filtered and duplicates removed


Sequence quality metrics (filtered/deduped BAM)

rep1
rep1
rep2
rep2

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)

rep1rep2ctl1
Total Fragments168649961442654656089165
Distinct Fragments147399821279884743899072
Positions with Two Read156228912194947518324
NRF = Distinct/Total0.8739990.8871730.782666
PBC1 = OneRead/Distinct0.8781340.891880.784732
PBC2 = OneRead/TwoRead8.2850749.3604654.582009

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


Replication quality metrics


IDR (Irreproducible Discovery Rate) plots

rep1_vs_rep2
rep1_vs_rep2
rep1-pr1_vs_rep1-pr2
rep1-pr1_vs_rep1-pr2
rep2-pr1_vs_rep2-pr2
rep2-pr1_vs_rep2-pr2
pooled-pr1_vs_pooled-pr2
pooled-pr1_vs_pooled-pr2

Reproducibility QC and peak detection statistics

overlapidr
Nt6676211
N16534136
N27005124
Np6331223
N optimal6676223
N conservative6676211
Optimal Setrep1_vs_rep2pooled-pr1_vs_pooled-pr2
Conservative Setrep1_vs_rep2rep1_vs_rep2
Rescue Ratio1.0544937608592641.0568720379146919
Self Consistency Ratio1.07208448117539021.096774193548387
Reproducibility Testpasspass

Reproducibility QC


Number of raw peaks

rep1rep2
Number of peaks2417816963

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics


Peak region size

rep1rep2idr_optoverlap_opt
Min size188.0251.0195.0195.0
25 percentile750.0816.0776.0776.0
50 percentile (median)750.0816.0776.0776.0
75 percentile750.0816.0776.0776.0
Max size3588.02792.03622.03622.0
Mean751.7483662833981816.5427106054353912.4215246636771780.2633313361295

rep1
rep1
rep2
rep2
idr_opt
idr_opt
overlap_opt
overlap_opt

Enrichment / Signal-to-noise ratio


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

rep1rep2
Number of Subsampled Reads1500000014426546
Estimated Fragment Length285300
Cross-correlation at Estimated Fragment Length0.8340053169733960.828932885097844
Phantom Peak5050
Cross-correlation at Phantom Peak0.83481810.8296212
Argmin of Cross-correlation15001500
Minimum of Cross-correlation0.83136250.8257135
NSC (Normalized Strand Cross-correlation coeff.)1.0031791.003899
RSC (Relative Strand Cross-correlation coeff.)0.76478550.8238497


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.


rep1
rep1
rep2
rep2

Jensen-Shannon distance (filtered/deduped BAM)

rep1rep2
AUC0.422247592653414050.41047754908288714
Synthetic AUC0.49766709295086470.49749647797563695
X-intercept0.028534677114444780.02865470520101704
Synthetic X-intercept0.00.0
Elbow Point0.38539818317486290.4220727650270163
Synthetic Elbow Point0.50141028318231370.49807101578266066
JS Distance0.0141442051111496330.02624001480190002
Synthetic JS Distance0.123084854173864470.13465314952213486
% Genome Enriched36.7528001552363238.82768567844876
Diff. Enrichment3.2389645167471674.17860243810585
CHANCE Divergence0.0276968418112687740.03552757502904798

Peak enrichment


Fraction of reads in peaks (FRiP)

FRiP for spp raw peaks

rep1rep2rep1-pr1rep2-pr1rep1-pr2rep2-pr2pooledpooled-pr1pooled-pr2
Fraction of Reads in Peaks0.18558897784866010.152743472193045350.183362717298249130.199375335750791060.165709028139082250.200579746607063650.138984825427898970.146083609464455420.15433812927774748

FRiP for overlap peaks

rep1_vs_rep2rep1-pr1_vs_rep1-pr2rep2-pr1_vs_rep2-pr2pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks0.055603345504356120.050906787485832610.063792104046614460.052324988867347745

FRiP for IDR peaks

rep1_vs_rep2rep1-pr1_vs_rep1-pr2rep2-pr1_vs_rep2-pr2pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks0.00377469267242626840.00292482145666855650.00300384780941435070.004004236754863966

For spp raw peaks:


For overlap/IDR peaks: