Input data and parameters
Input
| Analysis date: | Thu May 28 10:48:46 CST 2026 |
| BAM file: | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment/03_results/bam/WT_04.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: | 485,814 |
| Total number of alignments: | 564,420 |
| Number of secondary alignments: | 78,606 |
| Number of non-unique alignments: | 132,498 |
| Aligned to genes: | 355,413 |
| Ambiguous alignments: | 72,310 |
| No feature assigned: | 4,199 |
| Not aligned: | 14,186 |
| Strand specificity estimation (fwd/rev): | 0.51 / 0.49 |
Reads genomic origin
| Exonic: | 355,413 / 98.83% |
| Intronic: | 626 / 0.17% |
| Intergenic: | 3,573 / 0.99% |
| Intronic/intergenic overlapping exon: | 13,961 / 3.88% |
Transcript coverage profile
| 5' bias: | 0.24 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 1.17 |
Junction analysis
| Reads at junctions: | 4,064 |
| TGCT | 4.08% |
| CTCT | 3.37% |
| AGGT | 3.32% |
| AAAT | 3.08% |
| ACCT | 2.95% |
| TGGC | 2.73% |
| AAGC | 2.66% |
| AACC | 2.44% |
| ACGT | 2.39% |
| CTGC | 2.29% |
| TAGT | 2.26% |
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