Input data and parameters
Input
| Analysis date: | Tue Oct 31 10:08:41 GMT 2023 |
| BAM file: | SRX7354382.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): | 53,032,111 / 52,992,423 |
| Number of aligned pairs (without duplicates): | 52,970,654 |
| Total number of alignments: | 113,957,177 |
| Number of secondary alignments: | 7,932,643 |
| Number of non-unique alignments: | 13,359,686 |
| Aligned to genes: | 89,280,779 |
| Ambiguous alignments: | 330,588 |
| No feature assigned: | 10,400,524 |
| Missing chromosome in annotation: | 585,600 |
| Not aligned: | 2,532,034 |
Reads genomic origin
| Exonic: | 89,280,779 / 89.57% |
| Intronic: | 6,131,288 / 6.15% |
| Intergenic: | 4,269,236 / 4.28% |
| Intronic/intergenic overlapping exon: | 4,143,351 / 4.16% |
Transcript coverage profile
| 5' bias: | 0.39 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.75 |
Junction analysis
| Reads at junctions: | 29,720,911 |
| ACCT | 5.54% |
| AGGT | 4.51% |
| ATCT | 3.98% |
| TCCT | 3.87% |
| GCCT | 3.49% |
| AGGA | 3.11% |
| CCCT | 2.79% |
| AGCT | 2.45% |
| AGGC | 2.33% |
| TTCT | 2.2% |
| AGGG | 1.75% |
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