Input data and parameters
Input
| Analysis date: | Fri Jul 18 00:35:28 GMT 2025 |
| BAM file: | DE-3C.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): | 78,856,641 / 78,834,962 |
| Number of aligned pairs (without duplicates): | 78,811,152 |
| Total number of alignments: | 176,633,950 |
| Number of secondary alignments: | 18,942,347 |
| Number of non-unique alignments: | 27,805,748 |
| Aligned to genes: | 84,674,432 |
| Ambiguous alignments: | 633,267 |
| No feature assigned: | 63,513,059 |
| Missing chromosome in annotation: | 7,444 |
| Not aligned: | 0 |
Reads genomic origin
| Exonic: | 84,674,432 / 57.14% |
| Intronic: | 50,221,592 / 33.89% |
| Intergenic: | 13,291,467 / 8.97% |
| Intronic/intergenic overlapping exon: | 4,285,356 / 2.89% |
Transcript coverage profile
| 5' bias: | 0.58 |
| 3' bias: | 0.37 |
| 5'-3' bias: | 1.3 |
Junction analysis
| Reads at junctions: | 49,959,947 |
| AGGT | 8.58% |
| ACCT | 5.22% |
| AGGA | 3.36% |
| TCCT | 3.33% |
| ATCT | 3.03% |
| AGCT | 2.91% |
| GCCT | 2.63% |
| AGGC | 2.54% |
| CCCT | 2.34% |
| AGAT | 2.17% |
| AGGG | 2.16% |
.png)
.png)
.png)
