Input data and parameters
Input
| Analysis date: | Mon Oct 30 09:51:12 GMT 2023 |
| BAM file: | SRX7354064.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): | 58,435,666 / 58,324,439 |
| Number of aligned pairs (without duplicates): | 58,315,493 |
| Total number of alignments: | 125,651,064 |
| Number of secondary alignments: | 8,890,959 |
| Number of non-unique alignments: | 13,939,944 |
| Aligned to genes: | 90,511,023 |
| Ambiguous alignments: | 337,133 |
| No feature assigned: | 19,838,797 |
| Missing chromosome in annotation: | 1,024,167 |
| Not aligned: | 16,168,087 |
Reads genomic origin
| Exonic: | 90,511,023 / 82.02% |
| Intronic: | 12,266,614 / 11.12% |
| Intergenic: | 7,572,183 / 6.86% |
| Intronic/intergenic overlapping exon: | 3,985,199 / 3.61% |
Transcript coverage profile
| 5' bias: | 0.41 |
| 3' bias: | 0.32 |
| 5'-3' bias: | 1.72 |
Junction analysis
| Reads at junctions: | 35,141,538 |
| ACCT | 5.07% |
| AGGT | 4.6% |
| TCCT | 3.96% |
| ATCT | 3.74% |
| GCCT | 3.45% |
| AGGA | 3.23% |
| CCCT | 2.77% |
| AGCT | 2.69% |
| AGGC | 2.51% |
| TTCT | 2.21% |
| AGAT | 1.95% |

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