Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:14:52 GMT 2023 |
| BAM file: | SRX7354195.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): | 46,433,556 / 46,396,691 |
| Number of aligned pairs (without duplicates): | 46,384,014 |
| Total number of alignments: | 99,423,538 |
| Number of secondary alignments: | 6,593,291 |
| Number of non-unique alignments: | 10,511,485 |
| Aligned to genes: | 79,160,797 |
| Ambiguous alignments: | 285,822 |
| No feature assigned: | 8,829,560 |
| Missing chromosome in annotation: | 635,874 |
| Not aligned: | 3,948,711 |
Reads genomic origin
| Exonic: | 79,160,797 / 89.97% |
| Intronic: | 5,443,469 / 6.19% |
| Intergenic: | 3,386,091 / 3.85% |
| Intronic/intergenic overlapping exon: | 3,464,192 / 3.94% |
Transcript coverage profile
| 5' bias: | 0.23 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 2.09 |
Junction analysis
| Reads at junctions: | 25,141,832 |
| ACCT | 5.38% |
| AGGT | 4.69% |
| TCCT | 3.95% |
| ATCT | 3.79% |
| AGGA | 3.37% |
| GCCT | 2.95% |
| CCCT | 2.52% |
| AGCT | 2.38% |
| AGGC | 2.3% |
| TTCT | 2.04% |
| AGAT | 1.93% |
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