Input data and parameters
Input
| Analysis date: | Thu May 28 10:47:42 CST 2026 |
| BAM file: | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment/03_results/bam/SNF2KO_05.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: | 482,844 |
| Total number of alignments: | 548,678 |
| Number of secondary alignments: | 65,834 |
| Number of non-unique alignments: | 114,206 |
| Aligned to genes: | 359,443 |
| Ambiguous alignments: | 69,544 |
| No feature assigned: | 5,485 |
| Not aligned: | 17,156 |
| Strand specificity estimation (fwd/rev): | 0.51 / 0.49 |
Reads genomic origin
| Exonic: | 359,443 / 98.5% |
| Intronic: | 590 / 0.16% |
| Intergenic: | 4,895 / 1.34% |
| Intronic/intergenic overlapping exon: | 14,178 / 3.89% |
Transcript coverage profile
| 5' bias: | 0.24 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 1.17 |
Junction analysis
| Reads at junctions: | 3,301 |
| AGGT | 4.33% |
| TGCT | 4.09% |
| AAAT | 3.57% |
| AAGC | 3.24% |
| CTCT | 2.97% |
| AACC | 2.61% |
| ACCA | 2.57% |
| TGGC | 2.48% |
| ACGT | 2.27% |
| AGCC | 2.24% |
| ACCT | 2.21% |
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