Input data and parameters
Input
| Analysis date: | Tue Oct 31 10:04:10 GMT 2023 |
| BAM file: | SRX7354331.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): | 57,922,780 / 57,795,728 |
| Number of aligned pairs (without duplicates): | 57,781,796 |
| Total number of alignments: | 122,855,076 |
| Number of secondary alignments: | 7,136,568 |
| Number of non-unique alignments: | 11,349,271 |
| Aligned to genes: | 92,481,700 |
| Ambiguous alignments: | 356,800 |
| No feature assigned: | 17,946,866 |
| Missing chromosome in annotation: | 720,439 |
| Not aligned: | 27,840,528 |
Reads genomic origin
| Exonic: | 92,481,700 / 83.75% |
| Intronic: | 12,154,731 / 11.01% |
| Intergenic: | 5,792,135 / 5.25% |
| Intronic/intergenic overlapping exon: | 4,570,860 / 4.14% |
Transcript coverage profile
| 5' bias: | 0.45 |
| 3' bias: | 0.3 |
| 5'-3' bias: | 1.65 |
Junction analysis
| Reads at junctions: | 39,181,914 |
| ACCT | 5.15% |
| AGGT | 4.73% |
| TCCT | 3.7% |
| ATCT | 3.52% |
| AGGA | 3.37% |
| GCCT | 3.28% |
| AGCT | 2.77% |
| CCCT | 2.75% |
| AGGC | 2.51% |
| AGAT | 2.04% |
| TTCT | 2.04% |

.png)
.png)
.png)

