Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:52:48 GMT 2023 |
| BAM file: | SRX7354328.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): | 41,207,039 / 41,077,532 |
| Number of aligned pairs (without duplicates): | 41,055,031 |
| Total number of alignments: | 88,617,064 |
| Number of secondary alignments: | 6,332,493 |
| Number of non-unique alignments: | 10,661,547 |
| Aligned to genes: | 69,797,539 |
| Ambiguous alignments: | 262,704 |
| No feature assigned: | 7,575,172 |
| Missing chromosome in annotation: | 320,102 |
| Not aligned: | 7,747,195 |
Reads genomic origin
| Exonic: | 69,797,539 / 90.21% |
| Intronic: | 4,926,732 / 6.37% |
| Intergenic: | 2,648,440 / 3.42% |
| Intronic/intergenic overlapping exon: | 2,981,072 / 3.85% |
Transcript coverage profile
| 5' bias: | 0.23 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.76 |
Junction analysis
| Reads at junctions: | 22,527,070 |
| ACCT | 5.05% |
| AGGT | 4.74% |
| ATCT | 4.3% |
| TCCT | 3.7% |
| AGGA | 3.43% |
| GCCT | 2.93% |
| CCCT | 2.63% |
| AGCT | 2.37% |
| AGGC | 2.23% |
| TTCT | 2.18% |
| AGAA | 1.99% |

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