Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:42:56 GMT 2023 |
| BAM file: | SRX7354250.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): | 40,119,530 / 40,095,269 |
| Number of aligned pairs (without duplicates): | 40,091,153 |
| Total number of alignments: | 85,136,767 |
| Number of secondary alignments: | 4,921,968 |
| Number of non-unique alignments: | 7,899,604 |
| Aligned to genes: | 66,538,643 |
| Ambiguous alignments: | 272,396 |
| No feature assigned: | 9,935,478 |
| Missing chromosome in annotation: | 490,646 |
| Not aligned: | 3,188,711 |
Reads genomic origin
| Exonic: | 66,538,643 / 87.01% |
| Intronic: | 5,955,768 / 7.79% |
| Intergenic: | 3,979,710 / 5.2% |
| Intronic/intergenic overlapping exon: | 3,002,008 / 3.93% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.31 |
| 5'-3' bias: | 1.61 |
Junction analysis
| Reads at junctions: | 24,181,798 |
| ACCT | 5.12% |
| AGGT | 4.71% |
| ATCT | 3.62% |
| TCCT | 3.6% |
| GCCT | 3.43% |
| AGGA | 3.26% |
| CCCT | 2.68% |
| AGCT | 2.65% |
| AGGC | 2.48% |
| TTCT | 2.41% |
| AGAT | 1.92% |

.png)
.png)
.png)

