Input data and parameters
Input
| Analysis date: | Thu May 28 10:47:23 CST 2026 |
| BAM file: | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment/03_results/bam/SNF2KO_01.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: | 486,189 |
| Total number of alignments: | 543,925 |
| Number of secondary alignments: | 57,736 |
| Number of non-unique alignments: | 97,939 |
| Aligned to genes: | 367,835 |
| Ambiguous alignments: | 71,930 |
| No feature assigned: | 6,221 |
| Not aligned: | 13,811 |
| Strand specificity estimation (fwd/rev): | 0.51 / 0.49 |
Reads genomic origin
| Exonic: | 367,835 / 98.34% |
| Intronic: | 736 / 0.2% |
| Intergenic: | 5,485 / 1.47% |
| Intronic/intergenic overlapping exon: | 15,043 / 4.02% |
Transcript coverage profile
| 5' bias: | 0.28 |
| 3' bias: | 0.23 |
| 5'-3' bias: | 1.25 |
Junction analysis
| Reads at junctions: | 3,989 |
| TGCT | 4.06% |
| AGGT | 3.81% |
| AAAT | 2.91% |
| TGGC | 2.88% |
| CTCT | 2.81% |
| TCAC | 2.76% |
| ACCA | 2.73% |
| CTGC | 2.71% |
| AACC | 2.56% |
| ACGT | 2.38% |
| AAGC | 2.36% |
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