Input data and parameters
Input
| Analysis date: | Fri Jul 18 00:14:37 GMT 2025 |
| BAM file: | DE-7.markdup.sorted.bam |
| Counting algorithm: | uniquely-mapped-reads |
| GTF file: | genes.filtered.gtf |
| Number of bases for 5'-3' bias computation: | 100 |
| Number of transcripts for 5'-3' bias computation: | 1,000 |
| Paired-end sequencing: | yes |
| Protocol: | strand-specific-reverse |
| Sorting performed: | yes |
Summary
Reads alignment
| Number of mapped reads (left/right): | 68,589,471 / 68,569,869 |
| Number of aligned pairs (without duplicates): | 68,549,432 |
| Total number of alignments: | 153,734,631 |
| Number of secondary alignments: | 16,575,291 |
| Number of non-unique alignments: | 24,189,422 |
| Aligned to genes: | 70,425,497 |
| Ambiguous alignments: | 488,388 |
| No feature assigned: | 58,623,404 |
| Missing chromosome in annotation: | 7,920 |
| Not aligned: | 0 |
Reads genomic origin
| Exonic: | 70,425,497 / 54.57% |
| Intronic: | 46,558,520 / 36.08% |
| Intergenic: | 12,064,884 / 9.35% |
| Intronic/intergenic overlapping exon: | 3,454,924 / 2.68% |
Transcript coverage profile
| 5' bias: | 0.57 |
| 3' bias: | 0.36 |
| 5'-3' bias: | 1.31 |
Junction analysis
| Reads at junctions: | 40,457,753 |
| AGGT | 9.24% |
| ACCT | 4.99% |
| AGGA | 3.31% |
| TCCT | 3.27% |
| AGCT | 2.96% |
| ATCT | 2.91% |
| AGGC | 2.67% |
| GCCT | 2.54% |
| CCCT | 2.24% |
| AGGG | 2.21% |
| AGAT | 2.14% |
.png)
.png)
.png)
