| mapinsights genedepth -r reference.fa -i input.bam -o Genedepth-output/ -b 1000G_phase3_BRCA1.bed |
| Alignment file | input.bam |
| Reference file | reference.fa |
| Bed file | 1000G_phase3_BRCA1.bed |
| Analysis date | Fri Apr 8 15:45:59 2022 |
| No of contigs in alignment file | 86 |
| Reference size (bp) | 3137454505 |
| No of exones | 21 |
| Target bed size (bp) | 6635 |
| Mean depth of coverage | 23.69X |
| Exon no | Exon1 |
| Genomic coordinates | chr17:41201114-41201234 |
| Exon length (bp) | 121 |
| GC% | 44.63 |
| Mean depth of coverage | 27.83X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 100.00 |
| % covered with at least 10X depth | 100.00 |
| % covered with at least 20X depth | 100.00 |
| % covered with at least 30X depth | 28.93 |
| Exon no | Exon2 |
| Genomic coordinates | chr17:41203046-41203166 |
| Exon length (bp) | 121 |
| GC% | 55.37 |
| Mean depth of coverage | 18.56X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 100.00 |
| % covered with at least 10X depth | 95.04 |
| % covered with at least 20X depth | 51.24 |
| % covered with at least 30X depth | 0.00 |
| Exon no | Exon3 |
| Genomic coordinates | chr17:41209020-41209170 |
| Exon length (bp) | 151 |
| GC% | 46.36 |
| Mean depth of coverage | 55.42X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 100.00 |
| % covered with at least 10X depth | 100.00 |
| % covered with at least 20X depth | 100.00 |
| % covered with at least 30X depth | 100.00 |
| Exon no | Exon4 |
| Genomic coordinates | chr17:41215309-41215429 |
| Exon length (bp) | 121 |
| GC% | 35.54 |
| Mean depth of coverage | 11.98X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 90.08 |
| % covered with at least 10X depth | 74.38 |
| % covered with at least 20X depth | 0.00 |
| % covered with at least 30X depth | 0.00 |
| Exon no | Exon5 |
| Genomic coordinates | chr17:41215869-41215989 |
| Exon length (bp) | 121 |
| GC% | 37.19 |
| Mean depth of coverage | 8.92X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 100.00 |
| % covered with at least 10X depth | 47.11 |
| % covered with at least 20X depth | 0.00 |
| % covered with at least 30X depth | 0.00 |
| Exon no | Exon6 |
| Genomic coordinates | chr17:41219608-41219728 |
| Exon length (bp) | 121 |
| GC% | 33.06 |
| Mean depth of coverage | 38.79X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 100.00 |
| % covered with at least 10X depth | 100.00 |
| % covered with at least 20X depth | 100.00 |
| % covered with at least 30X depth | 76.03 |
| Exon no | Exon7 |
| Genomic coordinates | chr17:41222919-41223279 |
| Exon length (bp) | 361 |
| GC% | 46.81 |
| Mean depth of coverage | 6.20X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 44.60 |
| % covered with at least 10X depth | 24.93 |
| % covered with at least 20X depth | 0.00 |
| % covered with at least 30X depth | 0.00 |
| Exon no | Exon8 |
| Genomic coordinates | chr17:41226322-41226562 |
| Exon length (bp) | 241 |
| GC% | 43.57 |
| Mean depth of coverage | 32.60X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 96.27 |
| % covered with at least 10X depth | 87.14 |
| % covered with at least 20X depth | 67.63 |
| % covered with at least 30X depth | 59.75 |
| Exon no | Exon9 |
| Genomic coordinates | chr17:41228447-41228687 |
| Exon length (bp) | 241 |
| GC% | 34.85 |
| Mean depth of coverage | 33.42X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 100.00 |
| % covered with at least 10X depth | 99.59 |
| % covered with at least 20X depth | 74.27 |
| % covered with at least 30X depth | 54.77 |
| Exon no | Exon10 |
| Genomic coordinates | chr17:41231323-41231443 |
| Exon length (bp) | 121 |
| GC% | 40.50 |
| Mean depth of coverage | 49.07X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 100.00 |
| % covered with at least 10X depth | 100.00 |
| % covered with at least 20X depth | 100.00 |
| % covered with at least 30X depth | 100.00 |
| Exon no | Exon11 |
| Genomic coordinates | chr17:41234386-41234626 |
| Exon length (bp) | 241 |
| GC% | 43.98 |
| Mean depth of coverage | 18.49X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 86.72 |
| % covered with at least 10X depth | 68.88 |
| % covered with at least 20X depth | 44.81 |
| % covered with at least 30X depth | 22.41 |
| Exon no | Exon12 |
| Genomic coordinates | chr17:41242944-41243064 |
| Exon length (bp) | 121 |
| GC% | 43.80 |
| Mean depth of coverage | 37.89X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 100.00 |
| % covered with at least 10X depth | 100.00 |
| % covered with at least 20X depth | 100.00 |
| % covered with at least 30X depth | 83.47 |
| Exon no | Exon13 |
| Genomic coordinates | chr17:41243424-41246904 |
| Exon length (bp) | 3481 |
| GC% | 38.93 |
| Mean depth of coverage | 22.86X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 99.91 |
| % covered with at least 10X depth | 92.27 |
| % covered with at least 20X depth | 52.80 |
| % covered with at least 30X depth | 25.54 |
| Exon no | Exon14 |
| Genomic coordinates | chr17:41247840-41247960 |
| Exon length (bp) | 121 |
| GC% | 41.32 |
| Mean depth of coverage | 34.52X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 100.00 |
| % covered with at least 10X depth | 100.00 |
| % covered with at least 20X depth | 90.08 |
| % covered with at least 30X depth | 78.51 |
| Exon no | Exon15 |
| Genomic coordinates | chr17:41249223-41249343 |
| Exon length (bp) | 121 |
| GC% | 33.88 |
| Mean depth of coverage | 5.33X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 79.34 |
| % covered with at least 10X depth | 0.00 |
| % covered with at least 20X depth | 0.00 |
| % covered with at least 30X depth | 0.00 |
| Exon no | Exon16 |
| Genomic coordinates | chr17:41251784-41251904 |
| Exon length (bp) | 121 |
| GC% | 45.45 |
| Mean depth of coverage | 18.85X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 100.00 |
| % covered with at least 10X depth | 97.52 |
| % covered with at least 20X depth | 61.16 |
| % covered with at least 30X depth | 0.00 |
| Exon no | Exon17 |
| Genomic coordinates | chr17:41256104-41256328 |
| Exon length (bp) | 225 |
| GC% | 33.78 |
| Mean depth of coverage | 34.21X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 100.00 |
| % covered with at least 10X depth | 100.00 |
| % covered with at least 20X depth | 100.00 |
| % covered with at least 30X depth | 49.33 |
| Exon no | Exon18 |
| Genomic coordinates | chr17:41256868-41256988 |
| Exon length (bp) | 121 |
| GC% | 35.54 |
| Mean depth of coverage | 7.49X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 85.95 |
| % covered with at least 10X depth | 15.70 |
| % covered with at least 20X depth | 0.00 |
| % covered with at least 30X depth | 0.00 |
| Exon no | Exon19 |
| Genomic coordinates | chr17:41258451-41258571 |
| Exon length (bp) | 121 |
| GC% | 31.40 |
| Mean depth of coverage | 18.17X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 100.00 |
| % covered with at least 10X depth | 100.00 |
| % covered with at least 20X depth | 48.76 |
| % covered with at least 30X depth | 0.00 |
| Exon no | Exon20 |
| Genomic coordinates | chr17:41267709-41267829 |
| Exon length (bp) | 121 |
| GC% | 40.50 |
| Mean depth of coverage | 15.45X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 100.00 |
| % covered with at least 10X depth | 100.00 |
| % covered with at least 20X depth | 9.92 |
| % covered with at least 30X depth | 0.00 |
| Exon no | Exon21 |
| Genomic coordinates | chr17:41276013-41276133 |
| Exon length (bp) | 121 |
| GC% | 38.02 |
| Mean depth of coverage | 28.62X |
| % covered with at least 1X depth | 100.00 |
| % covered with at least 5X depth | 100.00 |
| % covered with at least 10X depth | 100.00 |
| % covered with at least 20X depth | 86.78 |
| % covered with at least 30X depth | 52.07 |