Input data and parameters
Input
| Analysis date: | Thu May 28 10:48:40 CST 2026 |
| BAM file: | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment/03_results/bam/WT_03.sorted.bam |
| Counting algorithm: | uniquely-mapped-reads |
| GTF file: | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/00_inputs/genes.gtf |
| Number of bases for 5'-3' bias computation: | 100 |
| Number of transcripts for 5'-3' bias computation: | 1,000 |
| Paired-end sequencing: | no |
| Protocol: | non-strand-specific |
| Sorting performed: | no |
Summary
Reads alignment
| Number of mapped reads: | 479,703 |
| Total number of alignments: | 559,977 |
| Number of secondary alignments: | 80,274 |
| Number of non-unique alignments: | 138,625 |
| Aligned to genes: | 344,668 |
| Ambiguous alignments: | 73,036 |
| No feature assigned: | 3,648 |
| Not aligned: | 20,297 |
| Strand specificity estimation (fwd/rev): | 0.5 / 0.5 |
Reads genomic origin
| Exonic: | 344,668 / 98.95% |
| Intronic: | 698 / 0.2% |
| Intergenic: | 2,950 / 0.85% |
| Intronic/intergenic overlapping exon: | 12,484 / 3.58% |
Transcript coverage profile
| 5' bias: | 0.33 |
| 3' bias: | 0.09 |
| 5'-3' bias: | 3.66 |
Junction analysis
| Reads at junctions: | 5,404 |
| TGCT | 4.05% |
| AGGT | 3.89% |
| TCAC | 3.22% |
| AAAT | 3.2% |
| CTCT | 2.98% |
| TGGC | 2.87% |
| ACGA | 2.33% |
| CTGC | 2.31% |
| ACGT | 2.29% |
| TAGT | 2.28% |
| AGAA | 2.2% |
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