Input data and parameters
Input
| Analysis date: | Tue Oct 31 15:38:32 GMT 2023 |
| BAM file: | SRX7354365.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): | 33,042,844 / 32,998,712 |
| Number of aligned pairs (without duplicates): | 32,994,763 |
| Total number of alignments: | 71,436,516 |
| Number of secondary alignments: | 5,394,960 |
| Number of non-unique alignments: | 9,233,275 |
| Aligned to genes: | 55,428,180 |
| Ambiguous alignments: | 188,446 |
| No feature assigned: | 6,265,686 |
| Missing chromosome in annotation: | 320,929 |
| Not aligned: | 6,163,986 |
Reads genomic origin
| Exonic: | 55,428,180 / 89.84% |
| Intronic: | 3,147,593 / 5.1% |
| Intergenic: | 3,118,093 / 5.05% |
| Intronic/intergenic overlapping exon: | 1,917,589 / 3.11% |
Transcript coverage profile
| 5' bias: | 0.26 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.95 |
Junction analysis
| Reads at junctions: | 16,378,852 |
| ACCT | 5.51% |
| AGGT | 4.52% |
| ATCT | 4.46% |
| TCCT | 3.66% |
| GCCT | 3.48% |
| AGGA | 3.27% |
| CCCT | 2.8% |
| AGCT | 2.46% |
| TTCT | 2.37% |
| AGGC | 2.28% |
| AGAT | 1.97% |

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