| Variant ID: vg0138594460 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 38594460 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GAAAGAGAGCGTAGAAATTCGAGTCACAACTCACAAGCTCAAATAAGCAAAGAAAACAAGAAATTAAGGCGTGCAGTAGATAATCGAGAGATGGAGATTG[C/G]
GATGAGCAGCAAGCGAGCGGAGGAGCTGGAGCAGCTGATCCAGCGGATGGAGCAGGCGGCGGCGCGTCGCCGGAAGACGCAGCCGGCGGGGAGCAAGCGC
GCGCTTGCTCCCCGCCGGCTGCGTCTTCCGGCGACGCGCCGCCGCCTGCTCCATCCGCTGGATCAGCTGCTCCAGCTCCTCCGCTCGCTTGCTGCTCATC[G/C]
CAATCTCCATCTCTCGATTATCTACTGCACGCCTTAATTTCTTGTTTTCTTTGCTTATTTGAGCTTGTGAGTTGTGACTCGAATTTCTACGCTCTCTTTC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.90% | 8.20% | 5.12% | 38.76% | NA |
| All Indica | 2759 | 42.90% | 0.10% | 3.04% | 54.01% | NA |
| All Japonica | 1512 | 64.60% | 25.30% | 9.72% | 0.46% | NA |
| Aus | 269 | 4.50% | 0.00% | 0.37% | 95.17% | NA |
| Indica I | 595 | 36.60% | 0.00% | 4.37% | 58.99% | NA |
| Indica II | 465 | 95.70% | 0.00% | 0.22% | 4.09% | NA |
| Indica III | 913 | 13.40% | 0.20% | 3.07% | 83.35% | NA |
| Indica Intermediate | 786 | 50.60% | 0.00% | 3.69% | 45.67% | NA |
| Temperate Japonica | 767 | 60.20% | 24.10% | 15.38% | 0.26% | NA |
| Tropical Japonica | 504 | 86.30% | 10.70% | 2.78% | 0.20% | NA |
| Japonica Intermediate | 241 | 32.80% | 59.30% | 6.22% | 1.66% | NA |
| VI/Aromatic | 96 | 32.30% | 0.00% | 5.21% | 62.50% | NA |
| Intermediate | 90 | 70.00% | 3.30% | 5.56% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0138594460 | C -> G | LOC_Os01g66480.1 | missense_variant ; p.Ala4Gly; MODERATE | nonsynonymous_codon ; A4G | Average:75.543; most accessible tissue: Callus, score: 97.025 | unknown | unknown | TOLERATED | 1.00 |
| vg0138594460 | C -> DEL | LOC_Os01g66480.1 | N | frameshift_variant | Average:75.543; most accessible tissue: Callus, score: 97.025 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0138594460 | 3.09E-06 | NA | mr1334 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0138594460 | NA | 6.19E-06 | mr1173_2 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0138594460 | 3.77E-07 | NA | mr1549_2 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0138594460 | 3.75E-06 | 1.08E-09 | mr1691_2 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |