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
| 1 | exNA19239mx2 | 2444 | 0.239974 | 83.14 | 37.5556 | 4.0644 | 36.9906 | 4.7998 |
| 2 | exNA19240mx2 | 1634 | 0.15966 | 92.41 | 37.3868 | 4.2164 | 36.8146 | 5.0853 |
| 3 | gilNA19240mx2 | 19894 | 1.931757 | 99.93 | 38.1249 | 4.0545 | 38.6194 | 2.8907 |
Alignment overview
| 1 | exNA19239mx2 | rdsbwa | 2444 | 2444 | 2444 | 100.00 | 412 | 2444 | 0.239974 | 99.98 | 55.56 |
| 2 | exNA19240mx2 | rdsbwa | 1634 | 1634 | 1634 | 100.00 | 124 | 1634 | 0.15966 | 99.97 | 63.80 |
| 3 | gilNA19240mx2 | rdsbwa | 19894 | 19894 | 19894 | 100.00 | 14 | 19894 | 1.931757 | 99.95 | 0.00 |
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
| 1 | exNA19239mx2 | rdsbwa | 64.190747 | 0.00 | 0.0082 | 0.0082 | 0.0078 | 0.0057 | 0.0026 |
| 2 | exNA19240mx2 | rdsbwa | 64.190747 | 0.00 | 0.0082 | 0.0082 | 0.0073 | 0.0035 | 0.0013 |
| 3 | gilNA19240mx2 | rdsbwa | 2897.310566 | 0.00 | 0.0017 | 0.0017 | 0.0017 | 0.0017 | 0.0015 |
Variants overview
| 1 | exNA19239mx2 | rdsbwa | gatkh | 12 | 5 | 0 | 2 | 3 | 4.00 |
| 2 | exNA19239mx2 | rdsbwa | strelka | 11 | 5 | 0 | 2 | 3 | 4.00 |
| 3 | exNA19240mx2 | rdsbwa | gatkh | 9 | 4 | 0 | 2 | 2 | 3.00 |
| 4 | exNA19240mx2 | rdsbwa | strelka | 9 | 4 | 0 | 2 | 2 | 3.00 |
| 5 | gilNA19240mx2 | rdsbwa | gatkh | 112 | 110 | 0 | 24 | 82 | 2.91 |
| 6 | gilNA19240mx2 | rdsbwa | strelka | 106 | 102 | 0 | 24 | 74 | 2.82 |
Gender prediction overview
| 1 | exNA19239mx2 | u | ? | ? | ? |
| 2 | exNA19240mx2 | u | ? | ? | ? |
| 3 | gilNA19240mx2 | u | ? | ? | ? |
Number of on-target bases with given depth
Number of off-target bases with given depth
fastqc overview
| 1 | exNA19239mx2 | forward | 53 | pass | pass | warn | fail | pass | warn | pass | warn |
| 2 | exNA19239mx2 | reverse | 53 | pass | pass | warn | fail | pass | warn | pass | warn |
| 3 | exNA19240mx2 | forward | 53 | pass | pass | pass | fail | pass | warn | pass | warn |
| 4 | exNA19240mx2 | reverse | 53 | pass | pass | warn | fail | pass | warn | pass | warn |
| 5 | gilNA19240mx2 | forward | 48 | pass | pass | pass | warn | pass | warn | pass | pass |
| 6 | gilNA19240mx2 | reverse | 48 | pass | pass | pass | fail | pass | warn | pass | pass |
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