Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:52:03 GMT 2023 |
| BAM file: | SRX7354288.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): | 52,671,655 / 52,643,361 |
| Number of aligned pairs (without duplicates): | 52,631,448 |
| Total number of alignments: | 113,282,305 |
| Number of secondary alignments: | 7,967,289 |
| Number of non-unique alignments: | 12,852,428 |
| Aligned to genes: | 91,808,008 |
| Ambiguous alignments: | 345,344 |
| No feature assigned: | 7,477,225 |
| Missing chromosome in annotation: | 799,300 |
| Not aligned: | 3,291,346 |
Reads genomic origin
| Exonic: | 91,808,008 / 92.47% |
| Intronic: | 4,544,381 / 4.58% |
| Intergenic: | 2,932,844 / 2.95% |
| Intronic/intergenic overlapping exon: | 4,240,469 / 4.27% |
Transcript coverage profile
| 5' bias: | 0.11 |
| 3' bias: | 0.15 |
| 5'-3' bias: | 1.86 |
Junction analysis
| Reads at junctions: | 29,203,516 |
| ACCT | 5.58% |
| ATCT | 4.78% |
| TCCT | 4.76% |
| AGGT | 4.28% |
| CCCT | 2.89% |
| AGGA | 2.8% |
| GCCT | 2.74% |
| AGGC | 2.4% |
| TCCC | 2.34% |
| AGCT | 2% |
| CGTA | 1.95% |

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