Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:30:33 GMT 2023 |
| BAM file: | SRX7354339.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): | 32,049,898 / 32,028,457 |
| Number of aligned pairs (without duplicates): | 32,025,030 |
| Total number of alignments: | 68,888,402 |
| Number of secondary alignments: | 4,810,047 |
| Number of non-unique alignments: | 8,288,904 |
| Aligned to genes: | 53,790,206 |
| Ambiguous alignments: | 207,994 |
| No feature assigned: | 6,377,061 |
| Missing chromosome in annotation: | 224,237 |
| Not aligned: | 7,175,313 |
Reads genomic origin
| Exonic: | 53,790,206 / 89.4% |
| Intronic: | 4,193,484 / 6.97% |
| Intergenic: | 2,183,577 / 3.63% |
| Intronic/intergenic overlapping exon: | 2,130,412 / 3.54% |
Transcript coverage profile
| 5' bias: | 0.34 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 2.39 |
Junction analysis
| Reads at junctions: | 18,463,519 |
| ACCT | 5.49% |
| AGGT | 4.67% |
| ATCT | 3.61% |
| AGGA | 3.51% |
| TCCT | 3.48% |
| GCCT | 3.25% |
| AGCT | 2.62% |
| CCCT | 2.42% |
| AGGC | 2.33% |
| AGAT | 2.19% |
| TTCT | 2.11% |
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