Input data and parameters
Input
| Analysis date: | Mon Oct 30 23:19:45 GMT 2023 |
| BAM file: | SRX7354280.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): | 71,928,397 / 71,870,885 |
| Number of aligned pairs (without duplicates): | 71,866,315 |
| Total number of alignments: | 152,381,753 |
| Number of secondary alignments: | 8,582,471 |
| Number of non-unique alignments: | 13,456,609 |
| Aligned to genes: | 121,875,632 |
| Ambiguous alignments: | 428,573 |
| No feature assigned: | 15,633,925 |
| Missing chromosome in annotation: | 987,014 |
| Not aligned: | 2,996,254 |
Reads genomic origin
| Exonic: | 121,875,632 / 88.63% |
| Intronic: | 10,067,722 / 7.32% |
| Intergenic: | 5,566,203 / 4.05% |
| Intronic/intergenic overlapping exon: | 4,981,885 / 3.62% |
Transcript coverage profile
| 5' bias: | 0.48 |
| 3' bias: | 0.15 |
| 5'-3' bias: | 2.22 |
Junction analysis
| Reads at junctions: | 50,756,574 |
| ACCT | 5.38% |
| AGGT | 4.79% |
| AGGA | 3.61% |
| ATCT | 3.55% |
| GCCT | 3.21% |
| TCCT | 3.18% |
| AGCT | 2.76% |
| AGGC | 2.46% |
| CCCT | 2.45% |
| TTCT | 2.29% |
| AGAT | 2.27% |

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