| Variant ID: vg0233325810 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 33325810 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 254. )
CTCTTCGCCGGCGGCATGGCAGGCAAGAGCTCGAGCTCGACACAGTCGTCGTCGTCTTCGTCGTCGTTGCTGCTGCGATTCAAGAAGCTCTCCTTGTGAT[C/G]
CAGAGATTGCTGTGAATTGAATTGTAAATGCGTGCAATTGGGTGGCGCGAGTGATATGATGCTAAGGCGGAGGCGGATCGCCGGTGCTTTGGCCGGTTTG
CAAACCGGCCAAAGCACCGGCGATCCGCCTCCGCCTTAGCATCATATCACTCGCGCCACCCAATTGCACGCATTTACAATTCAATTCACAGCAATCTCTG[G/C]
ATCACAAGGAGAGCTTCTTGAATCGCAGCAGCAACGACGACGAAGACGACGACGACTGTGTCGAGCTCGAGCTCTTGCCTGCCATGCCGCCGGCGAAGAG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.00% | 6.00% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 26.00% | 73.60% | 0.37% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 91.70% | 8.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0233325810 | C -> G | LOC_Os02g54370.1 | missense_variant ; p.Asp39His; MODERATE | nonsynonymous_codon ; D39H | Average:67.467; most accessible tissue: Zhenshan97 root, score: 82.361 | unknown | unknown | DELETERIOUS | 0.03 |