Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:15:34 GMT 2023 |
| BAM file: | SRX7354217.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): | 27,974,458 / 27,965,686 |
| Number of aligned pairs (without duplicates): | 27,964,013 |
| Total number of alignments: | 59,592,577 |
| Number of secondary alignments: | 3,652,433 |
| Number of non-unique alignments: | 5,906,644 |
| Aligned to genes: | 46,545,332 |
| Ambiguous alignments: | 158,744 |
| No feature assigned: | 6,591,651 |
| Missing chromosome in annotation: | 390,206 |
| Not aligned: | 881,478 |
Reads genomic origin
| Exonic: | 46,545,332 / 87.59% |
| Intronic: | 3,610,375 / 6.79% |
| Intergenic: | 2,981,276 / 5.61% |
| Intronic/intergenic overlapping exon: | 1,850,262 / 3.48% |
Transcript coverage profile
| 5' bias: | 0.44 |
| 3' bias: | 0.28 |
| 5'-3' bias: | 1.81 |
Junction analysis
| Reads at junctions: | 15,938,000 |
| ACCT | 5% |
| AGGT | 4.8% |
| TCCT | 3.54% |
| AGGA | 3.53% |
| ATCT | 3.49% |
| GCCT | 3.11% |
| AGCT | 2.77% |
| CCCT | 2.58% |
| AGGC | 2.44% |
| TTCT | 2.13% |
| AGAT | 2.08% |
.png)
.png)
.png)
