Input data and parameters
Input
| Analysis date: | Thu May 28 10:48:04 CST 2026 |
| BAM file: | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment/03_results/bam/SNF2KO_09.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: | 483,849 |
| Total number of alignments: | 544,149 |
| Number of secondary alignments: | 60,300 |
| Number of non-unique alignments: | 103,627 |
| Aligned to genes: | 362,944 |
| Ambiguous alignments: | 72,373 |
| No feature assigned: | 5,205 |
| Not aligned: | 16,151 |
| Strand specificity estimation (fwd/rev): | 0.51 / 0.49 |
Reads genomic origin
| Exonic: | 362,944 / 98.59% |
| Intronic: | 723 / 0.2% |
| Intergenic: | 4,482 / 1.22% |
| Intronic/intergenic overlapping exon: | 14,869 / 4.04% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.16 |
| 5'-3' bias: | 2.11 |
Junction analysis
| Reads at junctions: | 5,347 |
| TGCT | 4.6% |
| ACCA | 3.25% |
| AAAT | 3.14% |
| TCAC | 3.09% |
| TGGC | 2.92% |
| CTGC | 2.66% |
| AGCC | 2.6% |
| CTCT | 2.41% |
| ATGG | 2.39% |
| AGAC | 2.32% |
| AACC | 2.21% |
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