Input data and parameters
Input
| Analysis date: | Tue Oct 31 10:34:02 GMT 2023 |
| BAM file: | SRX7354333.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): | 93,225,169 / 93,121,755 |
| Number of aligned pairs (without duplicates): | 93,111,872 |
| Total number of alignments: | 199,686,523 |
| Number of secondary alignments: | 13,339,599 |
| Number of non-unique alignments: | 20,180,971 |
| Aligned to genes: | 147,666,855 |
| Ambiguous alignments: | 572,738 |
| No feature assigned: | 29,367,149 |
| Missing chromosome in annotation: | 1,898,810 |
| Not aligned: | 15,040,988 |
Reads genomic origin
| Exonic: | 147,666,855 / 83.41% |
| Intronic: | 17,610,531 / 9.95% |
| Intergenic: | 11,756,618 / 6.64% |
| Intronic/intergenic overlapping exon: | 7,082,759 / 4% |
Transcript coverage profile
| 5' bias: | 0.41 |
| 3' bias: | 0.3 |
| 5'-3' bias: | 1.77 |
Junction analysis
| Reads at junctions: | 69,055,608 |
| ACCT | 5.01% |
| AGGT | 4.93% |
| ATCT | 3.54% |
| TCCT | 3.53% |
| AGGA | 3.31% |
| GCCT | 2.8% |
| CCCT | 2.63% |
| AGCT | 2.62% |
| AGGC | 2.51% |
| TTCT | 2.32% |
| AGGG | 2.05% |
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