Input data and parameters
Input
| Analysis date: | Tue Oct 31 01:46:02 GMT 2023 |
| BAM file: | SRX7354273.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): | 56,403,401 / 56,389,292 |
| Number of aligned pairs (without duplicates): | 56,386,297 |
| Total number of alignments: | 122,383,193 |
| Number of secondary alignments: | 9,590,500 |
| Number of non-unique alignments: | 15,218,940 |
| Aligned to genes: | 80,785,428 |
| Ambiguous alignments: | 279,689 |
| No feature assigned: | 25,048,532 |
| Missing chromosome in annotation: | 1,050,604 |
| Not aligned: | 1,266,567 |
Reads genomic origin
| Exonic: | 80,785,428 / 76.33% |
| Intronic: | 11,892,032 / 11.24% |
| Intergenic: | 13,156,500 / 12.43% |
| Intronic/intergenic overlapping exon: | 3,434,460 / 3.25% |
Transcript coverage profile
| 5' bias: | 0.5 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.88 |
Junction analysis
| Reads at junctions: | 31,615,124 |
| ACCT | 4.79% |
| AGGT | 4.49% |
| ATCT | 3.67% |
| TCCT | 3.58% |
| AGGA | 3.39% |
| GCCT | 3.33% |
| CCCT | 2.71% |
| AGCT | 2.6% |
| TTCT | 2.44% |
| AGGC | 2.27% |
| AGAT | 2% |

.png)
.png)
.png)

