| Variant ID: vg0801635118 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 1635118 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GTCCCCCCTCGCCGGCGTGCCGGCGCCGGACCTGTCGAGGCACCTCGGCGAGCTGCTGGAGCGGGCGGACGGCGTGGGCGCGGACGTCACGTTCGACGTC[A/C]
GGGGGCAACCCTTCGCCGCCCACCGGATCGTGCTCGCCATGCGCTCGCCGGTGTTCATGGCATCGCTGTACGGGTCGATGAGGGAGCACCGCGCGCCGCG
CGCGGCGCGCGGTGCTCCCTCATCGACCCGTACAGCGATGCCATGAACACCGGCGAGCGCATGGCGAGCACGATCCGGTGGGCGGCGAAGGGTTGCCCCC[T/G]
GACGTCGAACGTGACGTCCGCGCCCACGCCGTCCGCCCGCTCCAGCAGCTCGCCGAGGTGCCTCGACAGGTCCGGCGCCGGCACGCCGGCGAGGGGGGAC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.00% | 5.20% | 0.06% | 0.70% | NA |
| All Indica | 2759 | 97.70% | 1.00% | 0.07% | 1.20% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 19.70% | 79.90% | 0.37% | 0.00% | NA |
| Indica I | 595 | 97.60% | 0.00% | 0.00% | 2.35% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.50% | 0.90% | 0.00% | 0.66% | NA |
| Indica Intermediate | 786 | 95.70% | 2.40% | 0.25% | 1.65% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0801635118 | A -> C | LOC_Os08g03490.1 | synonymous_variant ; p.Arg206Arg; LOW | synonymous_codon | Average:72.254; most accessible tissue: Zhenshan97 root, score: 83.259 | N | N | N | N |
| vg0801635118 | A -> DEL | LOC_Os08g03490.1 | N | frameshift_variant | Average:72.254; most accessible tissue: Zhenshan97 root, score: 83.259 | N | N | N | N |