Input data and parameters
Input
| Analysis date: | Mon Oct 30 12:59:07 GMT 2023 |
| BAM file: | SRX7354223.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): | 38,739,783 / 38,712,185 |
| Number of aligned pairs (without duplicates): | 38,707,237 |
| Total number of alignments: | 82,306,634 |
| Number of secondary alignments: | 4,854,666 |
| Number of non-unique alignments: | 8,203,238 |
| Aligned to genes: | 67,238,165 |
| Ambiguous alignments: | 250,829 |
| No feature assigned: | 6,333,840 |
| Missing chromosome in annotation: | 280,562 |
| Not aligned: | 5,575,590 |
Reads genomic origin
| Exonic: | 67,238,165 / 91.39% |
| Intronic: | 3,833,122 / 5.21% |
| Intergenic: | 2,500,718 / 3.4% |
| Intronic/intergenic overlapping exon: | 2,511,626 / 3.41% |
Transcript coverage profile
| 5' bias: | 0.32 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.64 |
Junction analysis
| Reads at junctions: | 22,673,084 |
| ACCT | 5.45% |
| AGGT | 4.74% |
| ATCT | 3.61% |
| TCCT | 3.47% |
| AGGA | 3.36% |
| GCCT | 3.18% |
| AGCT | 2.59% |
| AGGC | 2.41% |
| TTCT | 2.32% |
| CCCT | 2.31% |
| AGAT | 2.1% |
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