Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:53:20 GMT 2023 |
| BAM file: | SRX7354267.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): | 40,060,454 / 40,027,193 |
| Number of aligned pairs (without duplicates): | 40,022,528 |
| Total number of alignments: | 84,078,041 |
| Number of secondary alignments: | 3,990,394 |
| Number of non-unique alignments: | 6,962,113 |
| Aligned to genes: | 68,709,732 |
| Ambiguous alignments: | 189,588 |
| No feature assigned: | 8,022,791 |
| Missing chromosome in annotation: | 193,817 |
| Not aligned: | 5,885,935 |
Reads genomic origin
| Exonic: | 68,709,732 / 89.54% |
| Intronic: | 3,954,970 / 5.15% |
| Intergenic: | 4,067,821 / 5.3% |
| Intronic/intergenic overlapping exon: | 2,899,092 / 3.78% |
Transcript coverage profile
| 5' bias: | 0.36 |
| 3' bias: | 0.14 |
| 5'-3' bias: | 2.32 |
Junction analysis
| Reads at junctions: | 20,594,690 |
| ACCT | 5.57% |
| AGGT | 4.8% |
| AGGA | 3.68% |
| ATCT | 3.62% |
| TCCT | 3.45% |
| GCCT | 2.91% |
| AGCT | 2.69% |
| AGGC | 2.4% |
| AGAT | 2.34% |
| CCCT | 2.23% |
| TTCT | 2.17% |

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