Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:39:09 GMT 2023 |
| BAM file: | SRX7354313.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): | 46,129,012 / 46,097,352 |
| Number of aligned pairs (without duplicates): | 46,081,646 |
| Total number of alignments: | 102,923,380 |
| Number of secondary alignments: | 10,697,016 |
| Number of non-unique alignments: | 15,448,282 |
| Aligned to genes: | 76,809,627 |
| Ambiguous alignments: | 323,984 |
| No feature assigned: | 8,582,873 |
| Missing chromosome in annotation: | 1,758,614 |
| Not aligned: | 6,293,870 |
Reads genomic origin
| Exonic: | 76,809,627 / 89.95% |
| Intronic: | 4,911,703 / 5.75% |
| Intergenic: | 3,671,170 / 4.3% |
| Intronic/intergenic overlapping exon: | 3,282,615 / 3.84% |
Transcript coverage profile
| 5' bias: | 0.05 |
| 3' bias: | 0.09 |
| 5'-3' bias: | 2.51 |
Junction analysis
| Reads at junctions: | 19,910,452 |
| TCCT | 6.7% |
| CCCT | 6.21% |
| ACCT | 4.84% |
| ATCT | 4.83% |
| AGGT | 3.58% |
| AGGA | 2.81% |
| GTCT | 2.51% |
| TCCG | 2.11% |
| TTCT | 1.96% |
| AGGC | 1.93% |
| GCCT | 1.88% |

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