QC Report


general
Report generated at2022-12-26 17:34:47
Titleccch-3_OP628_youngadult_1_1
DescriptionENCSR514BBN
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 Reads156330461838168925335686
Paired Reads000
Unmapped Reads000
Unpaired Duplicate Reads201235922563133892462
Paired Duplicate Reads000
Paired Optical Duplicate Reads000
% Duplicate Reads12.872512.27479999999999915.3636

Filtered out (samtools view -F 1804):


SAMstat (filtered/deduped BAM)

rep1rep2ctl1
Total Reads136206871612537621443224
Total Reads (QC-failed)000
Duplicate Reads000
Duplicate Reads (QC-failed)000
Mapped Reads136206871612537621443224
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 Fragments154476721819534225038745
Distinct Fragments135980171610472921424709
Positions with Two Read143828216371482642456
NRF = Distinct/Total0.8802630.8851020.855662
PBC1 = OneRead/Distinct0.88080.8859780.85705
PBC2 = OneRead/TwoRead8.3273868.7154176.948856

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
Nt34662195
N11386937
N21239667
Np31749157
N optimal34662195
N conservative34662195
Optimal Setrep1_vs_rep2rep1_vs_rep2
Conservative Setrep1_vs_rep2rep1_vs_rep2
Rescue Ratio1.09175092128885941.2420382165605095
Self Consistency Ratio1.11882865440464661.8108108108108107
Reproducibility Testpasspass

Reproducibility QC


Number of raw peaks

rep1rep2
Number of peaks6309249003

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics


Peak region size

rep1rep2idr_optoverlap_opt
Min size600.0630.0206.0206.0
25 percentile600.0630.0610.0610.0
50 percentile (median)600.0630.0610.0610.0
75 percentile600.0630.0610.0610.0
Max size600.0630.0610.0610.0
Mean600.0630.0605.9025641025642609.9769488200335

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 Length205190
Cross-correlation at Estimated Fragment Length0.8343951563117010.840129990363163
Phantom Peak5050
Cross-correlation at Phantom Peak0.83487980.8407178
Argmin of Cross-correlation15001500
Minimum of Cross-correlation0.83126050.8370783
NSC (Normalized Strand Cross-correlation coeff.)1.0037711.003646
RSC (Relative Strand Cross-correlation coeff.)0.86608830.8384849


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
AUC0.419765041157388660.42231985796271393
Synthetic AUC0.49757195154729950.49776830265693445
X-intercept0.0286800814468798660.028600231564658442
Synthetic X-intercept0.00.0
Elbow Point0.396300954206092570.3851259631892043
Synthetic Elbow Point0.50021044096031650.4984986448317124
JS Distance0.0128333128078864660.009219687955897142
Synthetic JS Distance0.126804905807360060.12457787300148183
% Genome Enriched41.7020002395496541.64690382081687
Diff. Enrichment3.72015048054835653.3048474136817942
CHANCE Divergence0.0315999443911232840.028072489213762333

Peak enrichment


Fraction of reads in peaks (FRiP)

FRiP for spp raw peaks

rep1rep2rep1-pr1rep2-pr1rep1-pr2rep2-pr2pooledpooled-pr1pooled-pr2
Fraction of Reads in Peaks0.374025774177176250.308780210768418660.245075872819346560.22513372711433210.244371832666871540.228367636202715520.52528601852285460.318617078212431740.3398357066558928

FRiP for overlap peaks

rep1_vs_rep2rep1-pr1_vs_rep1-pr2rep2-pr1_vs_rep2-pr2pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks0.196666967322700840.087396105644304140.081272275449577120.1789417308771248

FRiP for IDR peaks

rep1_vs_rep2rep1-pr1_vs_rep1-pr2rep2-pr1_vs_rep2-pr2pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks0.00244691205017618640.00072911153453566620.0013530847280708370.0023407467401652445

For spp raw peaks:


For overlap/IDR peaks: