Input data and parameters
Input
| Analysis date: | Mon Oct 30 23:35:59 GMT 2023 |
| BAM file: | SRX7354242.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): | 65,926,347 / 65,890,423 |
| Number of aligned pairs (without duplicates): | 65,878,050 |
| Total number of alignments: | 142,754,241 |
| Number of secondary alignments: | 10,937,471 |
| Number of non-unique alignments: | 16,920,087 |
| Aligned to genes: | 112,579,920 |
| Ambiguous alignments: | 559,353 |
| No feature assigned: | 11,290,516 |
| Missing chromosome in annotation: | 1,404,365 |
| Not aligned: | 6,626,484 |
Reads genomic origin
| Exonic: | 112,579,920 / 90.89% |
| Intronic: | 5,675,082 / 4.58% |
| Intergenic: | 5,615,434 / 4.53% |
| Intronic/intergenic overlapping exon: | 5,488,616 / 4.43% |
Transcript coverage profile
| 5' bias: | 0.13 |
| 3' bias: | 0.13 |
| 5'-3' bias: | 2.21 |
Junction analysis
| Reads at junctions: | 43,454,013 |
| TCCT | 5.25% |
| ACCT | 4.9% |
| ATCT | 4.55% |
| AGGT | 4.38% |
| CCCT | 3.6% |
| AGGA | 2.93% |
| AGGC | 2.5% |
| GCCT | 2.3% |
| AGAC | 2.12% |
| TTCT | 2.02% |
| AGCT | 2% |
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