Input data and parameters
Input
| Analysis date: | Sun Oct 29 03:02:24 GMT 2023 |
| BAM file: | SRX7354167.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): | 27,184,429 / 27,169,038 |
| Number of aligned pairs (without duplicates): | 27,165,458 |
| Total number of alignments: | 57,747,406 |
| Number of secondary alignments: | 3,393,939 |
| Number of non-unique alignments: | 5,347,993 |
| Aligned to genes: | 45,421,498 |
| Ambiguous alignments: | 149,784 |
| No feature assigned: | 6,461,483 |
| Missing chromosome in annotation: | 366,648 |
| Not aligned: | 3,282,499 |
Reads genomic origin
| Exonic: | 45,421,498 / 87.55% |
| Intronic: | 4,005,263 / 7.72% |
| Intergenic: | 2,456,220 / 4.73% |
| Intronic/intergenic overlapping exon: | 2,028,546 / 3.91% |
Transcript coverage profile
| 5' bias: | 0.26 |
| 3' bias: | 0.23 |
| 5'-3' bias: | 1.66 |
Junction analysis
| Reads at junctions: | 13,495,509 |
| ACCT | 5.63% |
| AGGT | 4.49% |
| ATCT | 3.92% |
| TCCT | 3.85% |
| AGGA | 3.27% |
| GCCT | 3.24% |
| AGCT | 2.61% |
| CCCT | 2.59% |
| AGGC | 2.36% |
| AGAT | 2.04% |
| TTCT | 1.97% |

.png)
.png)
.png)

