| Variant ID: vg0327914592 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 27914592 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TGCCGTGAGCCGCCGTAGACCCGATCGATCTCGGCCGTCCGTTTTGGATGGATCGATCTCGGCCGTCCGTTTTGGATGGATCGATCTCGGCCGTCCGTTC[C/G]
CGTGAACCGCTGCCGTGCGCCTGGTCCACCGCAAAACCCTAGCCGCTGACGCAATAAATCCCTTTTTCCTTTTCAAAAATAATTCGTTATTGTGTCATAA
TTATGACACAATAACGAATTATTTTTGAAAAGGAAAAAGGGATTTATTGCGTCAGCGGCTAGGGTTTTGCGGTGGACCAGGCGCACGGCAGCGGTTCACG[G/C]
GAACGGACGGCCGAGATCGATCCATCCAAAACGGACGGCCGAGATCGATCCATCCAAAACGGACGGCCGAGATCGATCGGGTCTACGGCGGCTCACGGCA
| 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 | 83.40% | 0.20% | 6.16% | 10.24% | NA |
| All Indica | 2759 | 77.80% | 0.10% | 9.97% | 12.14% | NA |
| All Japonica | 1512 | 99.30% | 0.00% | 0.07% | 0.66% | NA |
| Aus | 269 | 55.40% | 1.50% | 2.23% | 40.89% | NA |
| Indica I | 595 | 65.50% | 0.00% | 15.46% | 18.99% | NA |
| Indica II | 465 | 68.00% | 0.00% | 9.68% | 22.37% | NA |
| Indica III | 913 | 91.50% | 0.10% | 4.16% | 4.27% | NA |
| Indica Intermediate | 786 | 77.10% | 0.10% | 12.72% | 10.05% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.41% | 0.83% | NA |
| VI/Aromatic | 96 | 76.00% | 3.10% | 6.25% | 14.58% | NA |
| Intermediate | 90 | 78.90% | 1.10% | 3.33% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0327914592 | C -> DEL | N | N | silent_mutation | Average:15.386; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0327914592 | C -> G | LOC_Os03g49010.1 | upstream_gene_variant ; 4095.0bp to feature; MODIFIER | silent_mutation | Average:15.386; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0327914592 | C -> G | LOC_Os03g49000.1 | intron_variant ; MODIFIER | silent_mutation | Average:15.386; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0327914592 | 7.31E-06 | NA | mr1016 | 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 |
| vg0327914592 | 4.09E-07 | NA | mr1022 | 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 |
| vg0327914592 | 1.58E-08 | NA | mr1055 | 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 |
| vg0327914592 | 5.66E-06 | NA | mr1079 | 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 |
| vg0327914592 | 5.46E-06 | NA | mr1390 | 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 |