| Variant ID: vg0318608683 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18608683 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGTAGTCCCAGCTGAGGACGATCTTGTGGAAGCGGTCCATGGTGGAGGCGGCGACGCCCGACGAGGAGGAGGAGGCGCCGCCTCCGCCTCCGCCGCCGCC[G/A]
GATTTGTCCACCGCCATTGGGGCGGCGGCGCGGCGGCGCGGCGGCGAGAGAAGGGGGTTCTGGGGTTTAGTGAGCCGCCGGCGCTGCAGCGGCAAACAGC
GCTGTTTGCCGCTGCAGCGCCGGCGGCTCACTAAACCCCAGAACCCCCTTCTCTCGCCGCCGCGCCGCCGCGCCGCCGCCCCAATGGCGGTGGACAAATC[C/T]
GGCGGCGGCGGAGGCGGAGGCGGCGCCTCCTCCTCCTCGTCGGGCGTCGCCGCCTCCACCATGGACCGCTTCCACAAGATCGTCCTCAGCTGGGACTACG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.30% | 2.00% | 1.12% | 0.57% | NA |
| All Indica | 2759 | 96.00% | 2.60% | 1.05% | 0.33% | NA |
| All Japonica | 1512 | 98.30% | 0.00% | 0.53% | 1.12% | NA |
| Aus | 269 | 85.90% | 8.60% | 5.58% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.00% | 0.50% | 0.00% | NA |
| Indica II | 465 | 97.40% | 0.40% | 0.65% | 1.51% | NA |
| Indica III | 913 | 94.10% | 5.00% | 0.88% | 0.00% | NA |
| Indica Intermediate | 786 | 94.90% | 2.90% | 1.91% | 0.25% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.00% | 0.00% | 1.59% | 3.37% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318608683 | G -> A | LOC_Os03g32526.1 | synonymous_variant ; p.Ser6Ser; LOW | synonymous_codon | Average:32.741; most accessible tissue: Minghui63 young leaf, score: 65.92 | N | N | N | N |
| vg0318608683 | G -> DEL | LOC_Os03g32526.1 | N | frameshift_variant | Average:32.741; most accessible tissue: Minghui63 young leaf, score: 65.92 | N | N | N | N |