Input data and parameters
Input
| Analysis date: | Fri Jul 18 01:39:15 GMT 2025 |
| BAM file: | DE-1.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): | 87,309,921 / 87,286,398 |
| Number of aligned pairs (without duplicates): | 87,258,574 |
| Total number of alignments: | 196,872,006 |
| Number of secondary alignments: | 22,275,687 |
| Number of non-unique alignments: | 33,760,422 |
| Aligned to genes: | 94,622,666 |
| Ambiguous alignments: | 704,333 |
| No feature assigned: | 67,777,956 |
| Missing chromosome in annotation: | 6,629 |
| Not aligned: | 0 |
Reads genomic origin
| Exonic: | 94,622,666 / 58.26% |
| Intronic: | 54,624,925 / 33.64% |
| Intergenic: | 13,153,031 / 8.1% |
| Intronic/intergenic overlapping exon: | 4,515,279 / 2.78% |
Transcript coverage profile
| 5' bias: | 0.56 |
| 3' bias: | 0.38 |
| 5'-3' bias: | 1.25 |
Junction analysis
| Reads at junctions: | 55,579,144 |
| ACCT | 5.77% |
| AGGT | 4.93% |
| AGGA | 3.62% |
| TCCT | 3.43% |
| AGGC | 3.04% |
| AGCT | 3.04% |
| ATCT | 2.96% |
| GCCT | 2.65% |
| CCCT | 2.43% |
| AGAT | 2.3% |
| AGGG | 2.28% |
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