Input data and parameters
Input
| Analysis date: | Thu May 28 10:47:37 CST 2026 |
| BAM file: | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment/03_results/bam/SNF2KO_04.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: | 491,150 |
| Total number of alignments: | 622,221 |
| Number of secondary alignments: | 131,071 |
| Number of non-unique alignments: | 240,457 |
| Aligned to genes: | 316,424 |
| Ambiguous alignments: | 60,446 |
| No feature assigned: | 4,894 |
| Not aligned: | 8,850 |
| Strand specificity estimation (fwd/rev): | 0.51 / 0.49 |
Reads genomic origin
| Exonic: | 316,424 / 98.48% |
| Intronic: | 528 / 0.16% |
| Intergenic: | 4,366 / 1.36% |
| Intronic/intergenic overlapping exon: | 12,679 / 3.95% |
Transcript coverage profile
| 5' bias: | 0.22 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 1.07 |
Junction analysis
| Reads at junctions: | 2,691 |
| TGCT | 3.72% |
| AGGT | 3.68% |
| ACGT | 3.42% |
| AAAT | 3.05% |
| AAGC | 2.82% |
| TGGC | 2.6% |
| AGCC | 2.6% |
| CTCT | 2.53% |
| ACCA | 2.53% |
| AGAA | 2.27% |
| CTTT | 2.23% |
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