Input data and parameters
Input
| Analysis date: | Mon Oct 30 11:18:12 GMT 2023 |
| BAM file: | SRX7354173.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): | 46,908,908 / 46,860,329 |
| Number of aligned pairs (without duplicates): | 46,830,217 |
| Total number of alignments: | 100,016,071 |
| Number of secondary alignments: | 6,246,834 |
| Number of non-unique alignments: | 10,192,217 |
| Aligned to genes: | 78,072,880 |
| Ambiguous alignments: | 316,938 |
| No feature assigned: | 10,912,637 |
| Missing chromosome in annotation: | 521,399 |
| Not aligned: | 2,987,145 |
Reads genomic origin
| Exonic: | 78,072,880 / 87.74% |
| Intronic: | 7,569,518 / 8.51% |
| Intergenic: | 3,343,119 / 3.76% |
| Intronic/intergenic overlapping exon: | 3,733,646 / 4.2% |
Transcript coverage profile
| 5' bias: | 0.46 |
| 3' bias: | 0.23 |
| 5'-3' bias: | 1.87 |
Junction analysis
| Reads at junctions: | 27,694,468 |
| ACCT | 5.04% |
| AGGT | 4.65% |
| ATCT | 3.57% |
| TCCT | 3.51% |
| AGGA | 3.45% |
| GCCT | 3.27% |
| AGCT | 2.81% |
| CCCT | 2.57% |
| AGGC | 2.41% |
| AGAT | 2.14% |
| TTCT | 2.12% |

.png)
.png)
.png)

