Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:20:35 GMT 2023 |
| BAM file: | SRX7354119.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): | 56,239,703 / 56,178,094 |
| Number of aligned pairs (without duplicates): | 56,171,379 |
| Total number of alignments: | 119,432,590 |
| Number of secondary alignments: | 7,014,793 |
| Number of non-unique alignments: | 11,549,460 |
| Aligned to genes: | 91,479,087 |
| Ambiguous alignments: | 293,944 |
| No feature assigned: | 15,503,741 |
| Missing chromosome in annotation: | 606,358 |
| Not aligned: | 8,841,247 |
Reads genomic origin
| Exonic: | 91,479,087 / 85.51% |
| Intronic: | 10,161,947 / 9.5% |
| Intergenic: | 5,341,794 / 4.99% |
| Intronic/intergenic overlapping exon: | 3,834,238 / 3.58% |
Transcript coverage profile
| 5' bias: | 0.32 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 1.82 |
Junction analysis
| Reads at junctions: | 26,477,875 |
| ACCT | 5.49% |
| AGGT | 4.81% |
| ATCT | 3.84% |
| AGGA | 3.59% |
| TCCT | 3.38% |
| GCCT | 3.31% |
| AGCT | 2.63% |
| CCCT | 2.56% |
| AGGC | 2.43% |
| AGAT | 2.3% |
| TTCT | 2.24% |

.png)
.png)
.png)

