QC Report


general
Report generated at2021-08-30 12:41:34
TitleF33H1.4_RW12303_youngadult_1_2
Descriptiongevirl
Pipeline versionv1.3.6
Pipeline typetf
GenomeWS245chr
Alignerbwa
Sequencing endedness{'rep1': {'paired_end': True}, 'rep2': {'paired_end': True}, 'ctl1': {'paired_end': True}, 'ctl2': {'paired_end': True}}
Peak callerspp

Alignment quality metrics


SAMstat (raw unfiltered BAM)

rep1rep2ctl1ctl2
Total Reads21551592189950122079557816447800
Total Reads (QC-failed)0000
Duplicate Reads0000
Duplicate Reads (QC-failed)0000
Mapped Reads21480894189385472073093316409571
Mapped Reads (QC-failed)0000
% Mapped Reads99.799.799.799.8
Paired Reads21551592189950122079557816447800
Paired Reads (QC-failed)0000
Read1107757969497506103977898223900
Read1 (QC-failed)0000
Read2107757969497506103977898223900
Read2 (QC-failed)0000
Properly Paired Reads21376298188701702061076416345026
Properly Paired Reads (QC-failed)0000
% Properly Paired Reads99.299.399.199.4
With itself21459960189234822070507216395710
With itself (QC-failed)0000
Singletons20934150652586113861
Singletons (QC-failed)0000
% Singleton0.10.10.10.1
Diff. Chroms756461343910211324
Diff. Chroms (QC-failed)0000

Marking duplicates (filtered BAM)

rep1rep2ctl1ctl2
Unpaired Reads0000
Paired Reads9795039868441294598047507946
Unmapped Reads0000
Unpaired Duplicate Reads0000
Paired Duplicate Reads174133012840321493279913909
Paired Optical Duplicate Reads159730121851141255106867
% Duplicate Reads17.777714.78549999999999915.78549999999999912.1726

Filtered out (samtools view -F 1804):


SAMstat (filtered/deduped BAM)

rep1rep2ctl1ctl2
Total Reads16107418148007601593305013188074
Total Reads (QC-failed)0000
Duplicate Reads0000
Duplicate Reads (QC-failed)0000
Mapped Reads16107418148007601593305013188074
Mapped Reads (QC-failed)0000
% Mapped Reads100.0100.0100.0100.0
Paired Reads16107418148007601593305013188074
Paired Reads (QC-failed)0000
Read18053709740038079665256594037
Read1 (QC-failed)0000
Read28053709740038079665256594037
Read2 (QC-failed)0000
Properly Paired Reads16107418148007601593305013188074
Properly Paired Reads (QC-failed)0000
% Properly Paired Reads100.0100.0100.0100.0
With itself16107418148007601593305013188074
With itself (QC-failed)0000
Singletons0000
Singletons (QC-failed)0000
% Singleton0.00.00.00.0
Diff. Chroms0000
Diff. Chroms (QC-failed)0000

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)

rep1rep2ctl1ctl2
Total Fragments9740837864339393696237434022
Distinct Fragments8017538737158879002856534148
Positions with Two Read12474489893291103313742304
NRF = Distinct/Total0.8230850.8528580.8431810.878952
PBC1 = OneRead/Distinct0.8170070.8477630.8387090.874892
PBC2 = OneRead/TwoRead5.2510286.3167636.0055897.701261

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
Nt314973165
N1235522219
N2216672733
Np310093250
N optimal314973250
N conservative314973165
Optimal Setrep1_vs_rep2pooled-pr1_vs_pooled-pr2
Conservative Setrep1_vs_rep2rep1_vs_rep2
Rescue Ratio1.01573736657099541.0268562401263823
Self Consistency Ratio1.0869986615590531.231635872014421
Reproducibility Testpasspass

Reproducibility QC


Number of raw peaks

rep1rep2
Number of peaks6761558604

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics


Peak region size

rep1rep2idr_optoverlap_opt
Min size78.085.085.085.0
25 percentile310.0340.0238.0340.0
50 percentile (median)310.0340.0340.0340.0
75 percentile310.0340.0340.0340.0
Max size771.0909.0933.0933.0
Mean308.52100865192637338.01527199508564300.9913846153846335.7991237260691

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 Reads91701478107005
Estimated Fragment Length155165
Cross-correlation at Estimated Fragment Length0.7242772683683070.713007108430159
Phantom Peak5555
Cross-correlation at Phantom Peak0.71498970.6959266
Argmin of Cross-correlation15001500
Minimum of Cross-correlation0.70216270.6757287
NSC (Normalized Strand Cross-correlation coeff.)1.0314951.055168
RSC (Relative Strand Cross-correlation coeff.)1.7240621.845657


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
AUC0.39556092159003330.3833856379536129
Synthetic AUC0.49840932441932280.49834402557357244
X-intercept0.019423483850361320.01939154389747275
Synthetic X-intercept0.00.0
Elbow Point0.5984868447319040.638248093584062
Synthetic Elbow Point0.50023208260234850.5019624596770786
JS Distance0.104481740590813530.13786657671355673
Synthetic JS Distance0.173087529275140540.19933580619647062
% Genome Enriched34.44224857268335430.09082924102687
Diff. Enrichment10.50806727876274512.246396003334503
CHANCE Divergence0.090317970777146770.10679047467004008

Peak enrichment


Fraction of reads in peaks (FRiP)

FRiP for spp raw peaks

rep1rep2rep1-pr1rep2-pr1rep1-pr2rep2-pr2pooledpooled-pr1pooled-pr2
Fraction of Reads in Peaks0.36742890760021250.36651894902694190.34757049856525750.357508398217388830.34185446008223790.36318580937735630.44295335040454340.379232746800361560.3501717474366653

FRiP for overlap peaks

rep1_vs_rep2rep1-pr1_vs_rep1-pr2rep2-pr1_vs_rep2-pr2pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks0.220539172512854040.169263751645359920.191076606876944170.21850003581576372

FRiP for IDR peaks

rep1_vs_rep2rep1-pr1_vs_rep1-pr2rep2-pr1_vs_rep2-pr2pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks0.06797634593666440.048461832926916030.076447290544539610.06877335182940904

For spp raw peaks:


For overlap/IDR peaks: