Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:32:03 GMT 2023 |
| BAM file: | SRX7354314.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): | 44,621,804 / 44,541,931 |
| Number of aligned pairs (without duplicates): | 44,519,442 |
| Total number of alignments: | 96,286,785 |
| Number of secondary alignments: | 7,123,050 |
| Number of non-unique alignments: | 11,214,189 |
| Aligned to genes: | 76,533,741 |
| Ambiguous alignments: | 332,960 |
| No feature assigned: | 7,527,045 |
| Missing chromosome in annotation: | 678,850 |
| Not aligned: | 5,872,927 |
Reads genomic origin
| Exonic: | 76,533,741 / 91.05% |
| Intronic: | 4,131,599 / 4.92% |
| Intergenic: | 3,395,446 / 4.04% |
| Intronic/intergenic overlapping exon: | 3,147,267 / 3.74% |
Transcript coverage profile
| 5' bias: | 0.1 |
| 3' bias: | 0.14 |
| 5'-3' bias: | 1.77 |
Junction analysis
| Reads at junctions: | 22,147,650 |
| TCCT | 5.27% |
| ACCT | 5.09% |
| ATCT | 4.57% |
| AGGT | 4.19% |
| CCCT | 3.49% |
| AGGA | 2.83% |
| GCCT | 2.39% |
| AGGC | 2.37% |
| TTCT | 2.1% |
| AGCT | 2.05% |
| AGAC | 1.92% |

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