Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:30:18 GMT 2023 |
| BAM file: | SRX7354222.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): | 40,893,502 / 40,631,754 |
| Number of aligned pairs (without duplicates): | 40,611,840 |
| Total number of alignments: | 87,391,881 |
| Number of secondary alignments: | 5,866,625 |
| Number of non-unique alignments: | 9,759,314 |
| Aligned to genes: | 58,940,846 |
| Ambiguous alignments: | 205,593 |
| No feature assigned: | 18,038,376 |
| Missing chromosome in annotation: | 447,752 |
| Not aligned: | 17,870,614 |
Reads genomic origin
| Exonic: | 58,940,846 / 76.57% |
| Intronic: | 8,827,496 / 11.47% |
| Intergenic: | 9,210,880 / 11.97% |
| Intronic/intergenic overlapping exon: | 3,676,854 / 4.78% |
Transcript coverage profile
| 5' bias: | 0.47 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.93 |
Junction analysis
| Reads at junctions: | 21,940,049 |
| ACCT | 5.29% |
| AGGT | 4.69% |
| TCCT | 3.5% |
| ATCT | 3.41% |
| GCCT | 3.34% |
| AGGA | 3.34% |
| AGCT | 2.78% |
| CCCT | 2.47% |
| AGGC | 2.39% |
| TTCT | 2.29% |
| AGAT | 2.14% |
.png)
.png)
.png)
