Input data and parameters
Input
| Analysis date: | Sun Oct 29 02:15:27 GMT 2023 |
| BAM file: | SRX7354090.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): | 35,951,248 / 35,923,173 |
| Number of aligned pairs (without duplicates): | 35,918,315 |
| Total number of alignments: | 77,329,337 |
| Number of secondary alignments: | 5,454,916 |
| Number of non-unique alignments: | 8,646,276 |
| Aligned to genes: | 59,400,127 |
| Ambiguous alignments: | 227,016 |
| No feature assigned: | 8,421,595 |
| Missing chromosome in annotation: | 634,323 |
| Not aligned: | 3,428,711 |
Reads genomic origin
| Exonic: | 59,400,127 / 87.58% |
| Intronic: | 5,015,247 / 7.39% |
| Intergenic: | 3,406,348 / 5.02% |
| Intronic/intergenic overlapping exon: | 2,438,599 / 3.6% |
Transcript coverage profile
| 5' bias: | 0.31 |
| 3' bias: | 0.28 |
| 5'-3' bias: | 1.63 |
Junction analysis
| Reads at junctions: | 22,125,176 |
| ACCT | 5.4% |
| AGGT | 4.35% |
| TCCT | 4.09% |
| ATCT | 3.92% |
| GCCT | 3.7% |
| AGGA | 3.03% |
| CCCT | 2.8% |
| AGCT | 2.51% |
| AGGC | 2.39% |
| TTCT | 2.2% |
| TCCC | 1.93% |
.png)
.png)
.png)
