Input data and parameters
Input
| Analysis date: | Mon Oct 30 09:39:56 GMT 2023 |
| BAM file: | SRX7354152.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): | 43,784,563 / 43,746,651 |
| Number of aligned pairs (without duplicates): | 43,740,530 |
| Total number of alignments: | 92,675,529 |
| Number of secondary alignments: | 5,144,315 |
| Number of non-unique alignments: | 8,626,931 |
| Aligned to genes: | 71,690,800 |
| Ambiguous alignments: | 251,499 |
| No feature assigned: | 11,763,025 |
| Missing chromosome in annotation: | 343,274 |
| Not aligned: | 8,634,736 |
Reads genomic origin
| Exonic: | 71,690,800 / 85.9% |
| Intronic: | 7,497,951 / 8.98% |
| Intergenic: | 4,265,074 / 5.11% |
| Intronic/intergenic overlapping exon: | 3,187,644 / 3.82% |
Transcript coverage profile
| 5' bias: | 0.3 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 1.79 |
Junction analysis
| Reads at junctions: | 22,059,751 |
| ACCT | 5.45% |
| AGGT | 4.74% |
| AGGA | 3.57% |
| ATCT | 3.5% |
| TCCT | 3.32% |
| GCCT | 3.13% |
| AGCT | 2.73% |
| AGGC | 2.43% |
| CCCT | 2.36% |
| AGAT | 2.36% |
| TTCT | 2.27% |
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