QC Report


general
Report generated at2022-12-19 18:37:20
Titlepha-2_OP687_lateembryonic_1_1
DescriptionENCSR164CYL
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 Reads178061961802715721377328
Paired Reads000
Unmapped Reads000
Unpaired Duplicate Reads252888527120533001570
Paired Duplicate Reads000
Paired Optical Duplicate Reads000
% Duplicate Reads14.20230000000000115.044314.0409

Filtered out (samtools view -F 1804):


SAMstat (filtered/deduped BAM)

rep1rep2ctl1
Total Reads152773111531510418375758
Total Reads (QC-failed)000
Duplicate Reads000
Duplicate Reads (QC-failed)000
Mapped Reads152773111531510418375758
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 Fragments177003371793627421302355
Distinct Fragments152583411529748018357831
Positions with Two Read178432418950782156017
NRF = Distinct/Total0.8620370.8528790.861775
PBC1 = OneRead/Distinct0.864520.8551360.864274
PBC2 = OneRead/TwoRead7.3927966.902847.359031

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
Nt7969563
N16967345
N26758260
Np8037531
N optimal8037563
N conservative7969563
Optimal Setpooled-pr1_vs_pooled-pr2rep1_vs_rep2
Conservative Setrep1_vs_rep2rep1_vs_rep2
Rescue Ratio1.00853306562931371.0602636534839924
Self Consistency Ratio1.0309263095590411.3269230769230769
Reproducibility Testpasspass

Reproducibility QC


Number of raw peaks

rep1rep2
Number of peaks1745615553

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics


Peak region size

rep1rep2idr_optoverlap_opt
Min size156.0153.0154.0154.0
25 percentile624.0604.0616.0616.0
50 percentile (median)624.0604.0616.0616.0
75 percentile624.0604.0616.0616.0
Max size624.0604.0616.0616.0
Mean623.4191681943172603.498553333762573.6110124333925613.0474057484136

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 Reads1500000015000000
Estimated Fragment Length215230
Cross-correlation at Estimated Fragment Length0.8341262317879740.83227556137894
Phantom Peak5050
Cross-correlation at Phantom Peak0.83437750.8324992
Argmin of Cross-correlation15001500
Minimum of Cross-correlation0.82950780.8276155
NSC (Normalized Strand Cross-correlation coeff.)1.0055681.005631
RSC (Relative Strand Cross-correlation coeff.)0.94840420.9542168


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
AUC0.404612178866270930.4037156690797016
Synthetic AUC0.49770717114220870.4977100689452387
X-intercept0.0284841913137594380.02851813910206103
Synthetic X-intercept0.00.0
Elbow Point0.48186489179641710.48074261785374095
Synthetic Elbow Point0.499702594751086640.5025445677857706
JS Distance0.0171518633407283620.016264288803372707
Synthetic JS Distance0.144327286574142870.1447911796819946
% Genome Enriched33.7834410676379734.71181323125034
Diff. Enrichment4.0432251652445913.981136453459555
CHANCE Divergence0.0346579887275887260.03402480109186733

Peak enrichment


Fraction of reads in peaks (FRiP)

FRiP for spp raw peaks

rep1rep2rep1-pr1rep2-pr1rep1-pr2rep2-pr2pooledpooled-pr1pooled-pr2
Fraction of Reads in Peaks0.137570937712795130.122824043506332050.1477254637465020.162355280120853230.151953583451536950.157894977402699980.146390567727327170.138755108455638150.13453838588873698

FRiP for overlap peaks

rep1_vs_rep2rep1-pr1_vs_rep1-pr2rep2-pr1_vs_rep2-pr2pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks0.065119017246595270.059797434247427440.0571142056887109640.06569036802096206

FRiP for IDR peaks

rep1_vs_rep2rep1-pr1_vs_rep1-pr2rep2-pr1_vs_rep2-pr2pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks0.008106159647742750.0057822348448624240.00452226769077114940.007641469298844174

For spp raw peaks:


For overlap/IDR peaks: