Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:25:24 GMT 2023 |
| BAM file: | SRX7354302.markdup.sorted.bam |
| Counting algorithm: | uniquely-mapped-reads |
| GTF file: | gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.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): | 32,278,872 / 32,243,660 |
| Number of aligned pairs (without duplicates): | 32,238,826 |
| Total number of alignments: | 68,736,447 |
| Number of secondary alignments: | 4,213,915 |
| Number of non-unique alignments: | 6,526,165 |
| Aligned to genes: | 52,789,240 |
| Ambiguous alignments: | 200,624 |
| No feature assigned: | 8,679,982 |
| Missing chromosome in annotation: | 540,436 |
| Not aligned: | 9,622,506 |
Reads genomic origin
| Exonic: | 52,789,240 / 85.88% |
| Intronic: | 5,342,589 / 8.69% |
| Intergenic: | 3,337,393 / 5.43% |
| Intronic/intergenic overlapping exon: | 2,264,367 / 3.68% |
Transcript coverage profile
| 5' bias: | 0.49 |
| 3' bias: | 0.29 |
| 5'-3' bias: | 1.73 |
Junction analysis
| Reads at junctions: | 20,024,551 |
| ACCT | 5.28% |
| AGGT | 4.65% |
| GCCT | 3.71% |
| TCCT | 3.6% |
| ATCT | 3.51% |
| AGGA | 3.24% |
| AGCT | 2.8% |
| CCCT | 2.7% |
| AGGC | 2.44% |
| TTCT | 2.24% |
| AGAT | 2.03% |
.png)
.png)
.png)
