Input data and parameters
Input
| Analysis date: | Thu May 28 10:48:56 CST 2026 |
| BAM file: | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment/03_results/bam/WT_06.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: | 487,482 |
| Total number of alignments: | 559,844 |
| Number of secondary alignments: | 72,362 |
| Number of non-unique alignments: | 121,594 |
| Aligned to genes: | 360,633 |
| Ambiguous alignments: | 72,879 |
| No feature assigned: | 4,738 |
| Not aligned: | 12,518 |
| Strand specificity estimation (fwd/rev): | 0.51 / 0.49 |
Reads genomic origin
| Exonic: | 360,633 / 98.7% |
| Intronic: | 826 / 0.23% |
| Intergenic: | 3,912 / 1.07% |
| Intronic/intergenic overlapping exon: | 14,117 / 3.86% |
Transcript coverage profile
| 5' bias: | 0.3 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 1.57 |
Junction analysis
| Reads at junctions: | 5,095 |
| TGCT | 4.08% |
| AAAT | 3.43% |
| TGGC | 3.32% |
| AGGT | 3.12% |
| CTGC | 3.02% |
| ACCA | 2.89% |
| AGCA | 2.67% |
| CTCT | 2.55% |
| TCAC | 2.53% |
| ACGT | 2.36% |
| AAGC | 2.1% |
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