Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:57:57 GMT 2023 |
| BAM file: | SRX7354109.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): | 45,462,120 / 45,413,785 |
| Number of aligned pairs (without duplicates): | 45,401,913 |
| Total number of alignments: | 96,206,842 |
| Number of secondary alignments: | 5,330,937 |
| Number of non-unique alignments: | 8,757,011 |
| Aligned to genes: | 75,424,820 |
| Ambiguous alignments: | 236,025 |
| No feature assigned: | 11,338,793 |
| Missing chromosome in annotation: | 450,193 |
| Not aligned: | 8,587,413 |
Reads genomic origin
| Exonic: | 75,424,820 / 86.93% |
| Intronic: | 6,582,804 / 7.59% |
| Intergenic: | 4,755,989 / 5.48% |
| Intronic/intergenic overlapping exon: | 3,386,627 / 3.9% |
Transcript coverage profile
| 5' bias: | 0.28 |
| 3' bias: | 0.16 |
| 5'-3' bias: | 1.78 |
Junction analysis
| Reads at junctions: | 23,191,804 |
| ACCT | 5.2% |
| AGGT | 4.69% |
| ATCT | 3.68% |
| AGGA | 3.66% |
| TCCT | 3.33% |
| GCCT | 3.07% |
| AGCT | 2.84% |
| AGGC | 2.37% |
| CCCT | 2.37% |
| AGAT | 2.28% |
| TTCT | 2.21% |

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