Input data and parameters
Input
| Analysis date: | Fri Jul 18 01:40:56 GMT 2025 |
| BAM file: | DE-6.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): | 89,064,449 / 89,032,378 |
| Number of aligned pairs (without duplicates): | 89,001,182 |
| Total number of alignments: | 203,249,203 |
| Number of secondary alignments: | 25,152,376 |
| Number of non-unique alignments: | 36,338,769 |
| Aligned to genes: | 85,197,788 |
| Ambiguous alignments: | 600,203 |
| No feature assigned: | 81,101,841 |
| Missing chromosome in annotation: | 10,602 |
| Not aligned: | 0 |
Reads genomic origin
| Exonic: | 85,197,788 / 51.23% |
| Intronic: | 65,873,809 / 39.61% |
| Intergenic: | 15,228,032 / 9.16% |
| Intronic/intergenic overlapping exon: | 4,426,978 / 2.66% |
Transcript coverage profile
| 5' bias: | 0.48 |
| 3' bias: | 0.29 |
| 5'-3' bias: | 1.43 |
Junction analysis
| Reads at junctions: | 50,118,718 |
| AGGT | 8.44% |
| ACCT | 5.11% |
| AGGA | 3.52% |
| TCCT | 3.46% |
| AGGC | 3.24% |
| AGCT | 3% |
| ATCT | 2.93% |
| GCCT | 2.51% |
| CCCT | 2.29% |
| AGAT | 2.25% |
| AGGG | 2.23% |
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