Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:23:50 GMT 2023 |
| BAM file: | SRX7354259.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): | 27,563,498 / 27,547,750 |
| Number of aligned pairs (without duplicates): | 27,545,396 |
| Total number of alignments: | 58,529,757 |
| Number of secondary alignments: | 3,418,509 |
| Number of non-unique alignments: | 5,649,810 |
| Aligned to genes: | 45,876,867 |
| Ambiguous alignments: | 161,165 |
| No feature assigned: | 6,587,530 |
| Missing chromosome in annotation: | 254,385 |
| Not aligned: | 2,233,346 |
Reads genomic origin
| Exonic: | 45,876,867 / 87.44% |
| Intronic: | 4,195,522 / 8% |
| Intergenic: | 2,392,008 / 4.56% |
| Intronic/intergenic overlapping exon: | 1,867,215 / 3.56% |
Transcript coverage profile
| 5' bias: | 0.36 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 2.03 |
Junction analysis
| Reads at junctions: | 13,621,676 |
| ACCT | 5.44% |
| AGGT | 4.83% |
| AGGA | 3.58% |
| ATCT | 3.54% |
| TCCT | 3.53% |
| GCCT | 3.03% |
| AGCT | 2.75% |
| CCCT | 2.57% |
| AGGC | 2.44% |
| AGAT | 2.3% |
| TTCT | 2.08% |

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