Input data and parameters
Input
| Analysis date: | Thu May 28 10:49:14 CST 2026 |
| BAM file: | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment/03_results/bam/WT_09.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: | 486,239 |
| Total number of alignments: | 566,570 |
| Number of secondary alignments: | 80,331 |
| Number of non-unique alignments: | 138,350 |
| Aligned to genes: | 344,181 |
| Ambiguous alignments: | 80,988 |
| No feature assigned: | 3,051 |
| Not aligned: | 13,761 |
| Strand specificity estimation (fwd/rev): | 0.51 / 0.49 |
Reads genomic origin
| Exonic: | 344,181 / 99.12% |
| Intronic: | 557 / 0.16% |
| Intergenic: | 2,494 / 0.72% |
| Intronic/intergenic overlapping exon: | 13,577 / 3.91% |
Transcript coverage profile
| 5' bias: | 0.27 |
| 3' bias: | 0.04 |
| 5'-3' bias: | 10.15 |
Junction analysis
| Reads at junctions: | 5,793 |
| TCAC | 4.57% |
| TGCT | 4.57% |
| ACCT | 3.47% |
| AGGT | 3.28% |
| CTCT | 3.26% |
| ACAC | 3.11% |
| ACGT | 3.02% |
| AAAT | 2.64% |
| ACCA | 2.5% |
| TTGG | 2.42% |
| CTGC | 2.38% |
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