Input data and parameters
Input
| Analysis date: | Thu May 28 10:48:10 CST 2026 |
| BAM file: | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment/03_results/bam/SNF2KO_10.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: | 483,852 |
| Total number of alignments: | 542,518 |
| Number of secondary alignments: | 58,666 |
| Number of non-unique alignments: | 101,156 |
| Aligned to genes: | 362,220 |
| Ambiguous alignments: | 74,207 |
| No feature assigned: | 4,935 |
| Not aligned: | 16,148 |
| Strand specificity estimation (fwd/rev): | 0.51 / 0.49 |
Reads genomic origin
| Exonic: | 362,220 / 98.66% |
| Intronic: | 763 / 0.21% |
| Intergenic: | 4,172 / 1.14% |
| Intronic/intergenic overlapping exon: | 14,478 / 3.94% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.11 |
| 5'-3' bias: | 3.11 |
Junction analysis
| Reads at junctions: | 6,373 |
| TGCT | 4.96% |
| TCAC | 3.7% |
| AAAT | 3.22% |
| CTGC | 2.89% |
| TGGC | 2.73% |
| AGAC | 2.71% |
| ACCA | 2.71% |
| CTCT | 2.68% |
| AGGT | 2.6% |
| AGCC | 2.46% |
| TTGG | 2.42% |
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