NGS reports exp mixed_yri_mx2

Experiment info

This report was generated by genomecomb version 0.106.0. It combines overview results on 3 samples of experiment mixed_yri_mx2

Yield and quality overview

#samplenumreadsnumbases-mbpct-unique-readsfw-qual-meanfw-qual-stdevrev-qual-meanrev-qual-stdev
1exNA19239mx224440.23997483.1437.55564.064436.99064.7998
2exNA19240mx216340.1596692.4137.38684.216436.81465.0853
3gilNA19240mx2198941.93175799.9338.12494.054538.61942.8907

Alignment overview

#samplealignmentnumalignmentsnumreadsmapped-readspct_mapped-readsduplicate-readsproperly-paired-readsnum-mapped-bases-mbpct-mapped-basespct-mapped-ontarget
1exNA19239mx2rdsbwa244424442444100.0041224440.23997499.9855.56
2exNA19240mx2rdsbwa163416341634100.0012416340.1596699.9763.80
3gilNA19240mx2rdsbwa198941989419894100.0014198941.93175799.950.00

Alignment target overview

no target region was supplied for rdsbwa-gilNA19240mx2. The full "sequenced genome" region in /complgen/refseq/hg19/extra/reg_hg19_sequencedgenome.tsv.zst was used as target region for calulations in the table
#samplealignmenttarget-region-mbavg-depth-ontargetpct-target-1Xpct-target-2Xpct-target-10Xpct-target-20Xpct-target-30X
1exNA19239mx2rdsbwa64.1907470.000.00820.00820.00780.00570.0026
2exNA19240mx2rdsbwa64.1907470.000.00820.00820.00730.00350.0013
3gilNA19240mx2rdsbwa2897.3105660.000.00170.00170.00170.00170.0015

Variants overview

#samplealignmentvarcallervarsqvarsqvars-refcodingqvars-zyg-mqvars-zyg-tqvars-TiTv-ratio
1exNA19239mx2rdsbwagatkh1250234.00
2exNA19239mx2rdsbwastrelka1150234.00
3exNA19240mx2rdsbwagatkh940223.00
4exNA19240mx2rdsbwastrelka940223.00
5gilNA19240mx2rdsbwagatkh112110024822.91
6gilNA19240mx2rdsbwastrelka106102024742.82

Gender prediction overview

#samplepredicted-genderY-over-X-rationormalised-Y-over-X-ratiopct-heterozygous-Y
1exNA19239mx2u???
2exNA19240mx2u???
3gilNA19240mx2u???

Number of on-target bases with given depth

Number of off-target bases with given depth

fastqc overview

#sampledirgcper-base-qualityper-sequence-qualityper-base-contentper-sequence-gcper-base-Nlength-distributionsequence-duplicationoverrepresented-seq
1exNA19239mx2forward53passpasswarnfailpasswarnpasswarn
2exNA19239mx2reverse53passpasswarnfailpasswarnpasswarn
3exNA19240mx2forward53passpasspassfailpasswarnpasswarn
4exNA19240mx2reverse53passpasswarnfailpasswarnpasswarn
5gilNA19240mx2forward48passpasspasswarnpasswarnpasspass
6gilNA19240mx2reverse48passpasspassfailpasswarnpasspass

Fastqc forward read quality per position (median and 10th percentile)

Fastqc reverse read quality per position (median and 10th percentile)

Fastqc forward reads per quality

Fastqc reverse reads per quality

Fastqc forward reads GC content

Fastqc reverse reads GC content

Fastqc forward reads length distribution

Fastqc reverse reads length distribution

Quality distribution

Readlength distribution