Input data and parameters
Input
| Analysis date: | Thu May 28 10:48:22 CST 2026 |
| BAM file: | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment/03_results/bam/SNF2KO_12.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: | 484,889 |
| Total number of alignments: | 539,910 |
| Number of secondary alignments: | 55,021 |
| Number of non-unique alignments: | 93,965 |
| Aligned to genes: | 368,078 |
| Ambiguous alignments: | 72,427 |
| No feature assigned: | 5,440 |
| Not aligned: | 15,111 |
| Strand specificity estimation (fwd/rev): | 0.51 / 0.49 |
Reads genomic origin
| Exonic: | 368,078 / 98.54% |
| Intronic: | 671 / 0.18% |
| Intergenic: | 4,769 / 1.28% |
| Intronic/intergenic overlapping exon: | 15,474 / 4.14% |
Transcript coverage profile
| 5' bias: | 0.24 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1 |
Junction analysis
| Reads at junctions: | 3,496 |
| AAAT | 3.66% |
| TGCT | 3.38% |
| AAGC | 3.26% |
| AGGT | 3.23% |
| TGGC | 3.12% |
| CTCT | 3% |
| TAGT | 2.69% |
| AACC | 2.6% |
| ACCA | 2.6% |
| CTGC | 2.4% |
| ACGT | 2.35% |
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