Input data and parameters
Input
| Analysis date: | Fri Jul 18 00:27:31 GMT 2025 |
| BAM file: | HB.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): | 75,371,867 / 75,344,465 |
| Number of aligned pairs (without duplicates): | 75,319,060 |
| Total number of alignments: | 171,984,511 |
| Number of secondary alignments: | 21,268,179 |
| Number of non-unique alignments: | 30,836,676 |
| Aligned to genes: | 74,866,738 |
| Ambiguous alignments: | 528,243 |
| No feature assigned: | 65,742,906 |
| Missing chromosome in annotation: | 9,948 |
| Not aligned: | 0 |
Reads genomic origin
| Exonic: | 74,866,738 / 53.24% |
| Intronic: | 52,762,156 / 37.52% |
| Intergenic: | 12,980,750 / 9.23% |
| Intronic/intergenic overlapping exon: | 3,915,719 / 2.78% |
Transcript coverage profile
| 5' bias: | 0.56 |
| 3' bias: | 0.37 |
| 5'-3' bias: | 1.31 |
Junction analysis
| Reads at junctions: | 41,983,162 |
| AGGT | 10.07% |
| ACCT | 4.97% |
| AGGA | 3.38% |
| TCCT | 3.29% |
| AGCT | 2.94% |
| ATCT | 2.85% |
| GCCT | 2.54% |
| AGGC | 2.51% |
| CCCT | 2.26% |
| AGGG | 2.22% |
| AGAT | 2.19% |
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