Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:58:28 GMT 2023 |
| BAM file: | SRX7354281.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): | 37,526,378 / 37,512,103 |
| Number of aligned pairs (without duplicates): | 37,506,184 |
| Total number of alignments: | 80,776,508 |
| Number of secondary alignments: | 5,738,027 |
| Number of non-unique alignments: | 9,339,493 |
| Aligned to genes: | 64,335,667 |
| Ambiguous alignments: | 242,768 |
| No feature assigned: | 6,352,539 |
| Missing chromosome in annotation: | 506,041 |
| Not aligned: | 3,729,815 |
Reads genomic origin
| Exonic: | 64,335,667 / 91.01% |
| Intronic: | 3,546,037 / 5.02% |
| Intergenic: | 2,806,502 / 3.97% |
| Intronic/intergenic overlapping exon: | 2,478,877 / 3.51% |
Transcript coverage profile
| 5' bias: | 0.22 |
| 3' bias: | 0.14 |
| 5'-3' bias: | 2.29 |
Junction analysis
| Reads at junctions: | 19,390,930 |
| ACCT | 5.09% |
| AGGT | 4.77% |
| ATCT | 4.32% |
| TCCT | 4.21% |
| AGGA | 3.29% |
| CCCT | 2.92% |
| GCCT | 2.83% |
| AGCT | 2.31% |
| AGGC | 2.22% |
| TTCT | 2.1% |
| AGAA | 1.99% |

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