Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:20:50 GMT 2023 |
| BAM file: | SRX7354105.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): | 50,061,270 / 50,020,465 |
| Number of aligned pairs (without duplicates): | 50,012,580 |
| Total number of alignments: | 106,422,720 |
| Number of secondary alignments: | 6,340,985 |
| Number of non-unique alignments: | 10,505,566 |
| Aligned to genes: | 84,025,171 |
| Ambiguous alignments: | 259,803 |
| No feature assigned: | 11,163,723 |
| Missing chromosome in annotation: | 468,457 |
| Not aligned: | 8,516,585 |
Reads genomic origin
| Exonic: | 84,025,171 / 88.27% |
| Intronic: | 6,685,446 / 7.02% |
| Intergenic: | 4,478,277 / 4.7% |
| Intronic/intergenic overlapping exon: | 3,323,879 / 3.49% |
Transcript coverage profile
| 5' bias: | 0.26 |
| 3' bias: | 0.12 |
| 5'-3' bias: | 2.3 |
Junction analysis
| Reads at junctions: | 27,747,968 |
| ACCT | 5.55% |
| AGGT | 4.65% |
| ATCT | 3.63% |
| AGGA | 3.61% |
| TCCT | 3.33% |
| GCCT | 3.22% |
| AGCT | 2.62% |
| AGGC | 2.37% |
| CCCT | 2.27% |
| AGAT | 2.25% |
| TTCT | 2.2% |

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