Input data and parameters
Input
| Analysis date: | Fri Jul 18 00:43:06 GMT 2025 |
| BAM file: | DE-3.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): | 80,822,391 / 80,796,797 |
| Number of aligned pairs (without duplicates): | 80,767,510 |
| Total number of alignments: | 179,036,830 |
| Number of secondary alignments: | 17,417,642 |
| Number of non-unique alignments: | 25,432,890 |
| Aligned to genes: | 78,217,196 |
| Ambiguous alignments: | 579,030 |
| No feature assigned: | 74,799,522 |
| Missing chromosome in annotation: | 8,192 |
| Not aligned: | 0 |
Reads genomic origin
| Exonic: | 78,217,196 / 51.12% |
| Intronic: | 61,570,472 / 40.24% |
| Intergenic: | 13,229,050 / 8.65% |
| Intronic/intergenic overlapping exon: | 4,235,563 / 2.77% |
Transcript coverage profile
| 5' bias: | 0.58 |
| 3' bias: | 0.36 |
| 5'-3' bias: | 1.31 |
Junction analysis
| Reads at junctions: | 45,530,061 |
| AGGT | 8.09% |
| ACCT | 5.28% |
| AGGA | 3.38% |
| TCCT | 3.36% |
| ATCT | 3.07% |
| AGCT | 2.94% |
| GCCT | 2.68% |
| AGGC | 2.62% |
| CCCT | 2.33% |
| AGAT | 2.2% |
| AGGG | 2.16% |
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