Input data and parameters
Input
| Analysis date: | Tue Oct 31 01:25:20 GMT 2023 |
| BAM file: | SRX7354308.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): | 35,229,330 / 35,184,606 |
| Number of aligned pairs (without duplicates): | 35,181,118 |
| Total number of alignments: | 75,243,595 |
| Number of secondary alignments: | 4,829,659 |
| Number of non-unique alignments: | 8,154,856 |
| Aligned to genes: | 58,393,474 |
| Ambiguous alignments: | 204,378 |
| No feature assigned: | 8,169,029 |
| Missing chromosome in annotation: | 321,858 |
| Not aligned: | 4,455,770 |
Reads genomic origin
| Exonic: | 58,393,474 / 87.73% |
| Intronic: | 5,111,403 / 7.68% |
| Intergenic: | 3,057,626 / 4.59% |
| Intronic/intergenic overlapping exon: | 2,177,958 / 3.27% |
Transcript coverage profile
| 5' bias: | 0.33 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 2.1 |
Junction analysis
| Reads at junctions: | 16,811,769 |
| ACCT | 5.17% |
| AGGT | 4.8% |
| ATCT | 3.81% |
| AGGA | 3.57% |
| TCCT | 3.37% |
| GCCT | 3.16% |
| AGCT | 2.77% |
| CCCT | 2.54% |
| AGGC | 2.44% |
| AGAT | 2.33% |
| TTCT | 2.1% |

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