Input data and parameters
Input
| Analysis date: | Thu May 28 10:48:16 CST 2026 |
| BAM file: | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment/03_results/bam/SNF2KO_11.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: | 480,337 |
| Total number of alignments: | 539,744 |
| Number of secondary alignments: | 59,407 |
| Number of non-unique alignments: | 101,584 |
| Aligned to genes: | 360,189 |
| Ambiguous alignments: | 73,089 |
| No feature assigned: | 4,882 |
| Not aligned: | 19,663 |
| Strand specificity estimation (fwd/rev): | 0.51 / 0.49 |
Reads genomic origin
| Exonic: | 360,189 / 98.66% |
| Intronic: | 538 / 0.15% |
| Intergenic: | 4,344 / 1.19% |
| Intronic/intergenic overlapping exon: | 14,457 / 3.96% |
Transcript coverage profile
| 5' bias: | 0.19 |
| 3' bias: | 0.16 |
| 5'-3' bias: | 1.12 |
Junction analysis
| Reads at junctions: | 3,312 |
| ACGT | 4.08% |
| AGGT | 4.02% |
| AAGC | 3.8% |
| TGCT | 3.74% |
| CTCT | 3.32% |
| AAAT | 3.05% |
| AGCC | 2.9% |
| AGAA | 2.57% |
| TCAC | 2.48% |
| ACCA | 2.45% |
| TAGT | 2.42% |
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