Input data and parameters
Input
| Analysis date: | Tue Oct 31 01:11:58 GMT 2023 |
| BAM file: | SRX7354275.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): | 38,745,906 / 38,727,893 |
| Number of aligned pairs (without duplicates): | 38,724,558 |
| Total number of alignments: | 81,724,604 |
| Number of secondary alignments: | 4,250,805 |
| Number of non-unique alignments: | 7,169,348 |
| Aligned to genes: | 65,205,167 |
| Ambiguous alignments: | 211,388 |
| No feature assigned: | 8,855,449 |
| Missing chromosome in annotation: | 283,252 |
| Not aligned: | 3,045,629 |
Reads genomic origin
| Exonic: | 65,205,167 / 88.04% |
| Intronic: | 5,370,701 / 7.25% |
| Intergenic: | 3,484,748 / 4.71% |
| Intronic/intergenic overlapping exon: | 2,623,014 / 3.54% |
Transcript coverage profile
| 5' bias: | 0.27 |
| 3' bias: | 0.15 |
| 5'-3' bias: | 1.88 |
Junction analysis
| Reads at junctions: | 20,231,531 |
| ACCT | 5.49% |
| AGGT | 4.77% |
| AGGA | 3.6% |
| ATCT | 3.55% |
| TCCT | 3.28% |
| GCCT | 3.18% |
| AGCT | 2.78% |
| AGGC | 2.4% |
| AGAT | 2.32% |
| CCCT | 2.32% |
| TTCT | 2.12% |
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