Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:53:05 GMT 2023 |
| BAM file: | SRX7354055.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): | 51,044,481 / 51,001,192 |
| Number of aligned pairs (without duplicates): | 50,986,108 |
| Total number of alignments: | 109,931,316 |
| Number of secondary alignments: | 7,885,643 |
| Number of non-unique alignments: | 12,852,376 |
| Aligned to genes: | 84,936,466 |
| Ambiguous alignments: | 330,641 |
| No feature assigned: | 11,116,317 |
| Missing chromosome in annotation: | 695,516 |
| Not aligned: | 2,076,971 |
Reads genomic origin
| Exonic: | 84,936,466 / 88.43% |
| Intronic: | 7,779,510 / 8.1% |
| Intergenic: | 3,336,807 / 3.47% |
| Intronic/intergenic overlapping exon: | 3,956,451 / 4.12% |
Transcript coverage profile
| 5' bias: | 0.48 |
| 3' bias: | 0.25 |
| 5'-3' bias: | 1.74 |
Junction analysis
| Reads at junctions: | 31,922,768 |
| ACCT | 5.49% |
| AGGT | 4.59% |
| ATCT | 3.69% |
| GCCT | 3.62% |
| TCCT | 3.56% |
| AGGA | 3.2% |
| CCCT | 2.69% |
| AGCT | 2.66% |
| AGGC | 2.38% |
| TTCT | 2.26% |
| AGAT | 1.97% |

.png)
.png)
.png)

