Input data and parameters
Input
| Analysis date: | Tue Oct 31 10:04:17 GMT 2023 |
| BAM file: | SRX7354351.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): | 40,163,752 / 40,122,610 |
| Number of aligned pairs (without duplicates): | 40,116,751 |
| Total number of alignments: | 84,958,960 |
| Number of secondary alignments: | 4,672,598 |
| Number of non-unique alignments: | 7,877,302 |
| Aligned to genes: | 66,056,398 |
| Ambiguous alignments: | 207,353 |
| No feature assigned: | 10,555,179 |
| Missing chromosome in annotation: | 262,728 |
| Not aligned: | 8,409,014 |
Reads genomic origin
| Exonic: | 66,056,398 / 86.22% |
| Intronic: | 7,162,990 / 9.35% |
| Intergenic: | 3,392,189 / 4.43% |
| Intronic/intergenic overlapping exon: | 2,691,737 / 3.51% |
Transcript coverage profile
| 5' bias: | 0.28 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 2.05 |
Junction analysis
| Reads at junctions: | 19,948,601 |
| ACCT | 5.43% |
| AGGT | 4.66% |
| ATCT | 3.67% |
| AGGA | 3.58% |
| TCCT | 3.36% |
| GCCT | 3.15% |
| AGCT | 2.72% |
| AGGC | 2.39% |
| AGAT | 2.34% |
| CCCT | 2.28% |
| TTCT | 2.2% |

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