Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:56:55 GMT 2023 |
| BAM file: | SRX7354325.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): | 59,848,435 / 59,804,695 |
| Number of aligned pairs (without duplicates): | 59,794,158 |
| Total number of alignments: | 129,845,037 |
| Number of secondary alignments: | 10,191,907 |
| Number of non-unique alignments: | 15,790,042 |
| Aligned to genes: | 100,950,740 |
| Ambiguous alignments: | 414,973 |
| No feature assigned: | 11,588,553 |
| Missing chromosome in annotation: | 1,100,729 |
| Not aligned: | 7,798,324 |
Reads genomic origin
| Exonic: | 100,950,740 / 89.7% |
| Intronic: | 6,257,046 / 5.56% |
| Intergenic: | 5,331,507 / 4.74% |
| Intronic/intergenic overlapping exon: | 4,848,282 / 4.31% |
Transcript coverage profile
| 5' bias: | 0.05 |
| 3' bias: | 0.07 |
| 5'-3' bias: | 2.8 |
Junction analysis
| Reads at junctions: | 32,715,761 |
| TCCT | 5.61% |
| ACCT | 4.9% |
| AGGT | 4.37% |
| ATCT | 4.18% |
| CCCT | 3.93% |
| AGGA | 3.29% |
| AGGC | 2.08% |
| TGCT | 1.98% |
| AGAC | 1.93% |
| AGCT | 1.83% |
| GTCT | 1.83% |

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