Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:32:30 GMT 2023 |
| BAM file: | SRX7354306.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): | 74,436,389 / 74,382,890 |
| Number of aligned pairs (without duplicates): | 74,373,190 |
| Total number of alignments: | 159,970,734 |
| Number of secondary alignments: | 11,151,455 |
| Number of non-unique alignments: | 16,050,091 |
| Aligned to genes: | 130,152,536 |
| Ambiguous alignments: | 592,704 |
| No feature assigned: | 11,231,764 |
| Missing chromosome in annotation: | 1,943,639 |
| Not aligned: | 4,123,807 |
Reads genomic origin
| Exonic: | 130,152,536 / 92.06% |
| Intronic: | 6,605,421 / 4.67% |
| Intergenic: | 4,626,343 / 3.27% |
| Intronic/intergenic overlapping exon: | 5,498,545 / 3.89% |
Transcript coverage profile
| 5' bias: | 0.16 |
| 3' bias: | 0.15 |
| 5'-3' bias: | 1.98 |
Junction analysis
| Reads at junctions: | 49,983,960 |
| ACCT | 5.27% |
| TCCT | 4.68% |
| AGGT | 4.32% |
| ATCT | 4.18% |
| CCCT | 3.2% |
| AGGA | 2.85% |
| AGGC | 2.45% |
| GCCT | 2.42% |
| AGCT | 2.14% |
| TTCT | 1.9% |
| GTCT | 1.84% |

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