Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:26:34 GMT 2023 |
| BAM file: | SRX7354206.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): | 48,798,369 / 48,759,299 |
| Number of aligned pairs (without duplicates): | 48,753,247 |
| Total number of alignments: | 103,147,508 |
| Number of secondary alignments: | 5,589,840 |
| Number of non-unique alignments: | 9,139,498 |
| Aligned to genes: | 81,187,506 |
| Ambiguous alignments: | 236,505 |
| No feature assigned: | 12,088,249 |
| Missing chromosome in annotation: | 495,750 |
| Not aligned: | 5,523,314 |
Reads genomic origin
| Exonic: | 81,187,506 / 87.04% |
| Intronic: | 7,517,512 / 8.06% |
| Intergenic: | 4,570,737 / 4.9% |
| Intronic/intergenic overlapping exon: | 3,503,395 / 3.76% |
Transcript coverage profile
| 5' bias: | 0.36 |
| 3' bias: | 0.16 |
| 5'-3' bias: | 1.97 |
Junction analysis
| Reads at junctions: | 24,540,697 |
| ACCT | 5.41% |
| AGGT | 4.95% |
| AGGA | 3.73% |
| ATCT | 3.62% |
| TCCT | 3.47% |
| GCCT | 2.96% |
| AGCT | 2.74% |
| AGGC | 2.5% |
| CCCT | 2.37% |
| AGAT | 2.33% |
| TTCT | 2.2% |
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