Input data and parameters
Input
| Analysis date: | Tue Oct 31 15:55:56 GMT 2023 |
| BAM file: | SRX7354392.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): | 44,727,881 / 44,703,078 |
| Number of aligned pairs (without duplicates): | 44,696,610 |
| Total number of alignments: | 95,141,445 |
| Number of secondary alignments: | 5,710,486 |
| Number of non-unique alignments: | 9,154,232 |
| Aligned to genes: | 73,332,745 |
| Ambiguous alignments: | 284,453 |
| No feature assigned: | 11,882,841 |
| Missing chromosome in annotation: | 487,174 |
| Not aligned: | 2,412,497 |
Reads genomic origin
| Exonic: | 73,332,745 / 86.06% |
| Intronic: | 9,145,377 / 10.73% |
| Intergenic: | 2,737,464 / 3.21% |
| Intronic/intergenic overlapping exon: | 3,176,893 / 3.73% |
Transcript coverage profile
| 5' bias: | 0.32 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.71 |
Junction analysis
| Reads at junctions: | 25,989,169 |
| ACCT | 5.17% |
| AGGT | 4.69% |
| AGGA | 3.56% |
| ATCT | 3.5% |
| TCCT | 3.38% |
| GCCT | 2.99% |
| AGCT | 2.82% |
| AGGC | 2.33% |
| AGAT | 2.32% |
| CCCT | 2.31% |
| TTCT | 2.26% |

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