Input data and parameters
Input
| Analysis date: | Sun Oct 29 02:04:53 GMT 2023 |
| BAM file: | SRX7354073.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): | 41,137,377 / 41,110,579 |
| Number of aligned pairs (without duplicates): | 41,107,353 |
| Total number of alignments: | 88,043,530 |
| Number of secondary alignments: | 5,795,574 |
| Number of non-unique alignments: | 9,455,229 |
| Aligned to genes: | 68,641,636 |
| Ambiguous alignments: | 254,839 |
| No feature assigned: | 9,340,537 |
| Missing chromosome in annotation: | 351,289 |
| Not aligned: | 2,753,522 |
Reads genomic origin
| Exonic: | 68,641,636 / 88.02% |
| Intronic: | 7,474,021 / 9.58% |
| Intergenic: | 1,866,516 / 2.39% |
| Intronic/intergenic overlapping exon: | 2,443,085 / 3.13% |
Transcript coverage profile
| 5' bias: | 0.4 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 1.99 |
Junction analysis
| Reads at junctions: | 25,364,238 |
| ACCT | 5.06% |
| AGGT | 4.3% |
| AGGG | 3.44% |
| AGGA | 3.31% |
| TCCT | 3.13% |
| ATCT | 3.11% |
| AGCT | 2.51% |
| CCCT | 2.49% |
| GCCT | 2.25% |
| AGGC | 2.09% |
| AGAT | 2.06% |

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