Input data and parameters
Input
| Analysis date: | Thu May 28 10:47:28 CST 2026 |
| BAM file: | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment/03_results/bam/SNF2KO_02.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: | 483,408 |
| Total number of alignments: | 577,713 |
| Number of secondary alignments: | 94,305 |
| Number of non-unique alignments: | 169,483 |
| Aligned to genes: | 334,139 |
| Ambiguous alignments: | 68,880 |
| No feature assigned: | 5,211 |
| Not aligned: | 16,592 |
| Strand specificity estimation (fwd/rev): | 0.51 / 0.49 |
Reads genomic origin
| Exonic: | 334,139 / 98.46% |
| Intronic: | 640 / 0.19% |
| Intergenic: | 4,571 / 1.35% |
| Intronic/intergenic overlapping exon: | 13,957 / 4.11% |
Transcript coverage profile
| 5' bias: | 0.28 |
| 3' bias: | 0.16 |
| 5'-3' bias: | 1.82 |
Junction analysis
| Reads at junctions: | 4,194 |
| TGCT | 4.32% |
| AGGT | 3.55% |
| AAAT | 3.53% |
| ACGT | 3.46% |
| TGGC | 3.03% |
| CTCT | 2.89% |
| CTGC | 2.79% |
| ACCA | 2.53% |
| TCAC | 2.5% |
| AAGC | 2.43% |
| TAGT | 2.38% |
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