Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:24:05 GMT 2023 |
| BAM file: | SRX7354165.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): | 46,366,482 / 46,339,236 |
| Number of aligned pairs (without duplicates): | 46,334,477 |
| Total number of alignments: | 98,372,911 |
| Number of secondary alignments: | 5,667,193 |
| Number of non-unique alignments: | 9,641,837 |
| Aligned to genes: | 75,389,476 |
| Ambiguous alignments: | 195,146 |
| No feature assigned: | 12,769,900 |
| Missing chromosome in annotation: | 376,552 |
| Not aligned: | 5,059,886 |
Reads genomic origin
| Exonic: | 75,389,476 / 85.51% |
| Intronic: | 7,132,760 / 8.09% |
| Intergenic: | 5,637,140 / 6.39% |
| Intronic/intergenic overlapping exon: | 3,385,638 / 3.84% |
Transcript coverage profile
| 5' bias: | 0.25 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 2.01 |
Junction analysis
| Reads at junctions: | 16,440,295 |
| ACCT | 5.14% |
| AGGT | 4.7% |
| ATCT | 3.99% |
| TCCT | 3.71% |
| AGGA | 3.65% |
| GCCT | 2.91% |
| CCCT | 2.63% |
| AGCT | 2.54% |
| AGGC | 2.36% |
| TTCT | 2.24% |
| AGAT | 2.23% |

.png)
.png)
.png)

