| Variant ID: vg0224035929 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 24035929 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGAAGAGGAGCACCACACTCCACATTAGCCACTTGAGCTGCTTGGTCAGAGGCTTGAGCTTGCGCGTCAATGGCATCTTTGCGGGATTCGGACATACGCC[G/A]
TATAGCATGACGAGCCTTGGAAGAGGGAGAGCGACCTTGAGAACTCATTGACCCACGGCGAGAGTAAAGTTGATTCTTGAACTGACCCCTGATCATGAGG
CCTCATGATCAGGGGTCAGTTCAAGAATCAACTTTACTCTCGCCGTGGGTCAATGAGTTCTCAAGGTCGCTCTCCCTCTTCCAAGGCTCGTCATGCTATA[C/T]
GGCGTATGTCCGAATCCCGCAAAGATGCCATTGACGCGCAAGCTCAAGCCTCTGACCAAGCAGCTCAAGTGGCTAATGTGGAGTGTGGTGCTCCTCTTCC
| 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 | 42.70% | 0.50% | 31.95% | 24.82% | NA |
| All Indica | 2759 | 16.60% | 0.70% | 46.43% | 36.35% | NA |
| All Japonica | 1512 | 95.20% | 0.10% | 1.79% | 2.98% | NA |
| Aus | 269 | 17.10% | 0.00% | 63.94% | 18.96% | NA |
| Indica I | 595 | 16.50% | 0.50% | 42.86% | 40.17% | NA |
| Indica II | 465 | 10.80% | 0.20% | 52.04% | 36.99% | NA |
| Indica III | 913 | 19.60% | 0.40% | 46.11% | 33.84% | NA |
| Indica Intermediate | 786 | 16.50% | 1.30% | 46.18% | 36.01% | NA |
| Temperate Japonica | 767 | 97.90% | 0.00% | 0.65% | 1.43% | NA |
| Tropical Japonica | 504 | 89.90% | 0.00% | 4.17% | 5.95% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.40% | 0.41% | 1.66% | NA |
| VI/Aromatic | 96 | 24.00% | 5.20% | 15.62% | 55.21% | NA |
| Intermediate | 90 | 58.90% | 1.10% | 16.67% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0224035929 | G -> A | LOC_Os02g39780.1 | missense_variant ; p.Arg1228Trp; MODERATE | nonsynonymous_codon ; R1228W | Average:14.828; most accessible tissue: Callus, score: 47.459 | unknown | unknown | DELETERIOUS | 0.03 |
| vg0224035929 | G -> DEL | LOC_Os02g39780.1 | N | frameshift_variant | Average:14.828; most accessible tissue: Callus, score: 47.459 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0224035929 | 1.26E-07 | NA | mr1916 | 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 |
| vg0224035929 | 4.51E-08 | 4.51E-08 | mr1916 | Ind_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 |
| vg0224035929 | NA | 5.45E-06 | mr1563_2 | Ind_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 |