Input data and parameters
Input
| Analysis date: | Fri Jul 18 00:34:52 GMT 2025 |
| BAM file: | DE-5.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): | 79,518,941 / 79,489,396 |
| Number of aligned pairs (without duplicates): | 79,463,438 |
| Total number of alignments: | 179,299,009 |
| Number of secondary alignments: | 20,290,672 |
| Number of non-unique alignments: | 29,685,007 |
| Aligned to genes: | 77,053,238 |
| Ambiguous alignments: | 548,580 |
| No feature assigned: | 72,003,855 |
| Missing chromosome in annotation: | 8,329 |
| Not aligned: | 0 |
Reads genomic origin
| Exonic: | 77,053,238 / 51.69% |
| Intronic: | 58,629,076 / 39.33% |
| Intergenic: | 13,374,779 / 8.97% |
| Intronic/intergenic overlapping exon: | 3,979,962 / 2.67% |
Transcript coverage profile
| 5' bias: | 0.55 |
| 3' bias: | 0.35 |
| 5'-3' bias: | 1.35 |
Junction analysis
| Reads at junctions: | 45,044,548 |
| AGGT | 9.79% |
| ACCT | 5.1% |
| TCCT | 3.39% |
| AGGA | 3.38% |
| ATCT | 3.02% |
| AGCT | 2.95% |
| GCCT | 2.56% |
| AGGC | 2.44% |
| CCCT | 2.37% |
| AGAT | 2.16% |
| AGGG | 2.14% |
.png)
.png)
.png)
