Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:52:26 GMT 2023 |
| BAM file: | SRX7354361.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): | 26,929,969 / 26,913,475 |
| Number of aligned pairs (without duplicates): | 26,911,681 |
| Total number of alignments: | 57,201,849 |
| Number of secondary alignments: | 3,358,405 |
| Number of non-unique alignments: | 5,703,861 |
| Aligned to genes: | 44,822,964 |
| Ambiguous alignments: | 155,899 |
| No feature assigned: | 6,341,256 |
| Missing chromosome in annotation: | 177,869 |
| Not aligned: | 1,221,126 |
Reads genomic origin
| Exonic: | 44,822,964 / 87.61% |
| Intronic: | 4,420,807 / 8.64% |
| Intergenic: | 1,920,449 / 3.75% |
| Intronic/intergenic overlapping exon: | 1,713,221 / 3.35% |
Transcript coverage profile
| 5' bias: | 0.39 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.85 |
Junction analysis
| Reads at junctions: | 14,353,434 |
| ACCT | 5.27% |
| AGGT | 4.6% |
| ATCT | 3.74% |
| TCCT | 3.54% |
| AGGA | 3.53% |
| GCCT | 3.23% |
| AGCT | 2.71% |
| CCCT | 2.47% |
| AGGC | 2.36% |
| AGAT | 2.24% |
| TTCT | 2.09% |

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