Input data and parameters
Input
| Analysis date: | Mon Oct 30 09:23:48 GMT 2023 |
| BAM file: | SRX7354156.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): | 31,285,813 / 31,266,266 |
| Number of aligned pairs (without duplicates): | 31,263,886 |
| Total number of alignments: | 66,202,406 |
| Number of secondary alignments: | 3,650,327 |
| Number of non-unique alignments: | 6,012,280 |
| Aligned to genes: | 51,603,353 |
| Ambiguous alignments: | 171,049 |
| No feature assigned: | 8,137,511 |
| Missing chromosome in annotation: | 278,213 |
| Not aligned: | 1,318,855 |
Reads genomic origin
| Exonic: | 51,603,353 / 86.38% |
| Intronic: | 5,672,063 / 9.49% |
| Intergenic: | 2,465,448 / 4.13% |
| Intronic/intergenic overlapping exon: | 1,982,629 / 3.32% |
Transcript coverage profile
| 5' bias: | 0.41 |
| 3' bias: | 0.16 |
| 5'-3' bias: | 2.24 |
Junction analysis
| Reads at junctions: | 16,710,064 |
| ACCT | 5.37% |
| AGGT | 4.69% |
| AGGA | 3.63% |
| ATCT | 3.63% |
| TCCT | 3.37% |
| GCCT | 3.1% |
| AGCT | 2.74% |
| AGGC | 2.42% |
| AGAT | 2.4% |
| CCCT | 2.38% |
| TTCT | 2.26% |

.png)
.png)
.png)

