Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:22:42 GMT 2023 |
| BAM file: | SRX7354277.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): | 50,223,727 / 50,181,474 |
| Number of aligned pairs (without duplicates): | 50,162,522 |
| Total number of alignments: | 107,944,856 |
| Number of secondary alignments: | 7,539,655 |
| Number of non-unique alignments: | 12,629,491 |
| Aligned to genes: | 80,107,205 |
| Ambiguous alignments: | 286,846 |
| No feature assigned: | 14,445,370 |
| Missing chromosome in annotation: | 475,944 |
| Not aligned: | 5,527,373 |
Reads genomic origin
| Exonic: | 80,107,205 / 84.72% |
| Intronic: | 10,571,629 / 11.18% |
| Intergenic: | 3,873,741 / 4.1% |
| Intronic/intergenic overlapping exon: | 4,344,347 / 4.59% |
Transcript coverage profile
| 5' bias: | 0.27 |
| 3' bias: | 0.13 |
| 5'-3' bias: | 1.85 |
Junction analysis
| Reads at junctions: | 26,480,840 |
| ACCT | 5.32% |
| AGGT | 4.71% |
| AGGA | 3.61% |
| ATCT | 3.53% |
| TCCT | 3.31% |
| GCCT | 3.27% |
| AGCT | 2.77% |
| AGAT | 2.35% |
| CCCT | 2.34% |
| AGGC | 2.33% |
| TTCT | 2.26% |
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