Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:12:59 GMT 2023 |
| BAM file: | SRX7354214.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): | 38,645,621 / 38,633,136 |
| Number of aligned pairs (without duplicates): | 38,630,238 |
| Total number of alignments: | 82,519,718 |
| Number of secondary alignments: | 5,240,961 |
| Number of non-unique alignments: | 8,492,067 |
| Aligned to genes: | 65,131,153 |
| Ambiguous alignments: | 205,688 |
| No feature assigned: | 8,281,375 |
| Missing chromosome in annotation: | 409,435 |
| Not aligned: | 910,395 |
Reads genomic origin
| Exonic: | 65,131,153 / 88.72% |
| Intronic: | 5,993,149 / 8.16% |
| Intergenic: | 2,288,226 / 3.12% |
| Intronic/intergenic overlapping exon: | 2,199,483 / 3% |
Transcript coverage profile
| 5' bias: | 0.39 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 1.87 |
Junction analysis
| Reads at junctions: | 22,694,642 |
| ACCT | 5.06% |
| AGGT | 4.99% |
| AGGA | 3.94% |
| TCCT | 3.68% |
| ATCT | 3.43% |
| AGCT | 2.95% |
| GCCT | 2.43% |
| AGAT | 2.35% |
| AGGC | 2.35% |
| CCCT | 2.21% |
| TTCT | 2.04% |
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