Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:48:08 GMT 2023 |
| BAM file: | SRX7354367.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): | 36,812,997 / 36,790,647 |
| Number of aligned pairs (without duplicates): | 36,787,653 |
| Total number of alignments: | 77,810,803 |
| Number of secondary alignments: | 4,207,159 |
| Number of non-unique alignments: | 7,156,647 |
| Aligned to genes: | 62,278,552 |
| Ambiguous alignments: | 191,211 |
| No feature assigned: | 7,932,149 |
| Missing chromosome in annotation: | 252,244 |
| Not aligned: | 3,510,024 |
Reads genomic origin
| Exonic: | 62,278,552 / 88.7% |
| Intronic: | 4,993,491 / 7.11% |
| Intergenic: | 2,938,658 / 4.19% |
| Intronic/intergenic overlapping exon: | 2,293,994 / 3.27% |
Transcript coverage profile
| 5' bias: | 0.31 |
| 3' bias: | 0.16 |
| 5'-3' bias: | 2.12 |
Junction analysis
| Reads at junctions: | 18,914,375 |
| ACCT | 5.43% |
| AGGT | 4.69% |
| ATCT | 3.7% |
| AGGA | 3.56% |
| TCCT | 3.37% |
| GCCT | 3.34% |
| AGCT | 2.71% |
| AGGC | 2.34% |
| AGAT | 2.29% |
| CCCT | 2.27% |
| TTCT | 2.2% |

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