Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:07:55 GMT 2023 |
| BAM file: | SRX7354320.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): | 30,429,675 / 30,410,992 |
| Number of aligned pairs (without duplicates): | 30,406,980 |
| Total number of alignments: | 64,907,002 |
| Number of secondary alignments: | 4,066,335 |
| Number of non-unique alignments: | 6,801,018 |
| Aligned to genes: | 50,778,741 |
| Ambiguous alignments: | 169,429 |
| No feature assigned: | 6,879,064 |
| Missing chromosome in annotation: | 278,750 |
| Not aligned: | 2,218,915 |
Reads genomic origin
| Exonic: | 50,778,741 / 88.07% |
| Intronic: | 4,870,302 / 8.45% |
| Intergenic: | 2,008,762 / 3.48% |
| Intronic/intergenic overlapping exon: | 1,891,562 / 3.28% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.94 |
Junction analysis
| Reads at junctions: | 17,660,136 |
| ACCT | 5.16% |
| AGGT | 4.96% |
| ATCT | 3.77% |
| AGGA | 3.73% |
| TCCT | 3.55% |
| AGCT | 2.84% |
| GCCT | 2.83% |
| AGGC | 2.4% |
| CCCT | 2.3% |
| AGAT | 2.25% |
| TTCT | 2.05% |
.png)
.png)
.png)
