Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:08:55 GMT 2023 |
| BAM file: | SRX7354324.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): | 35,684,245 / 35,643,785 |
| Number of aligned pairs (without duplicates): | 35,637,204 |
| Total number of alignments: | 76,468,431 |
| Number of secondary alignments: | 5,140,401 |
| Number of non-unique alignments: | 8,989,813 |
| Aligned to genes: | 60,862,463 |
| Ambiguous alignments: | 215,512 |
| No feature assigned: | 6,167,100 |
| Missing chromosome in annotation: | 233,543 |
| Not aligned: | 8,454,642 |
Reads genomic origin
| Exonic: | 60,862,463 / 90.8% |
| Intronic: | 3,335,197 / 4.98% |
| Intergenic: | 2,831,903 / 4.22% |
| Intronic/intergenic overlapping exon: | 2,751,990 / 4.11% |
Transcript coverage profile
| 5' bias: | 0.23 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 1.9 |
Junction analysis
| Reads at junctions: | 19,397,255 |
| ACCT | 5.77% |
| AGGT | 4.76% |
| ATCT | 3.76% |
| TCCT | 3.7% |
| GCCT | 3.36% |
| AGGA | 3.29% |
| CCCT | 2.54% |
| AGCT | 2.42% |
| AGGC | 2.39% |
| TTCT | 2.24% |
| AGAT | 1.99% |

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