Input data and parameters
Input
| Analysis date: | Thu May 28 10:47:32 CST 2026 |
| BAM file: | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment/03_results/bam/SNF2KO_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: | 483,721 |
| Total number of alignments: | 539,633 |
| Number of secondary alignments: | 55,912 |
| Number of non-unique alignments: | 95,940 |
| Aligned to genes: | 366,796 |
| Ambiguous alignments: | 71,557 |
| No feature assigned: | 5,340 |
| Not aligned: | 16,279 |
| Strand specificity estimation (fwd/rev): | 0.52 / 0.48 |
Reads genomic origin
| Exonic: | 366,796 / 98.57% |
| Intronic: | 816 / 0.22% |
| Intergenic: | 4,524 / 1.22% |
| Intronic/intergenic overlapping exon: | 14,892 / 4% |
Transcript coverage profile
| 5' bias: | 0.39 |
| 3' bias: | 0.15 |
| 5'-3' bias: | 2.54 |
Junction analysis
| Reads at junctions: | 5,978 |
| TGCT | 4.48% |
| AAAT | 3.35% |
| ACCA | 3.25% |
| TGGC | 2.83% |
| TCAC | 2.78% |
| CTGC | 2.76% |
| AGGT | 2.73% |
| AGCC | 2.54% |
| AGAC | 2.33% |
| CTCT | 2.14% |
| TTGG | 2.09% |
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