Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:30:11 GMT 2023 |
| BAM file: | SRX7354257.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): | 37,371,332 / 37,350,980 |
| Number of aligned pairs (without duplicates): | 37,347,737 |
| Total number of alignments: | 79,305,212 |
| Number of secondary alignments: | 4,582,900 |
| Number of non-unique alignments: | 6,988,597 |
| Aligned to genes: | 60,971,233 |
| Ambiguous alignments: | 197,631 |
| No feature assigned: | 10,487,770 |
| Missing chromosome in annotation: | 659,981 |
| Not aligned: | 1,455,100 |
Reads genomic origin
| Exonic: | 60,971,233 / 85.32% |
| Intronic: | 6,599,593 / 9.24% |
| Intergenic: | 3,888,177 / 5.44% |
| Intronic/intergenic overlapping exon: | 2,936,962 / 4.11% |
Transcript coverage profile
| 5' bias: | 0.49 |
| 3' bias: | 0.25 |
| 5'-3' bias: | 1.89 |
Junction analysis
| Reads at junctions: | 23,168,261 |
| ACCT | 5.31% |
| AGGT | 4.68% |
| TCCT | 3.68% |
| ATCT | 3.57% |
| AGGA | 3.37% |
| GCCT | 3.3% |
| AGCT | 2.74% |
| CCCT | 2.62% |
| AGGC | 2.45% |
| TTCT | 2.27% |
| AGAT | 2.19% |

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