| Variant ID: vg1112990301 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 12990301 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.04, others allele: 0.00, population size: 218. )
GGAAGTGGTGAGTGGTGACGACGATGCTCATCCGGAAGATACGGTGTATGATTCCAGTGGCTATATTGACACACCAGCTACAAGGCAAGCACAGCTACGA[C/T]
GTCACCTACGCACAAACCGCACAGGTATGGGTGGCACTCGCCACCAACAAGGTAATAATAATCGTGTGCCCGATTATCCTTATGCTATGGTTATGTTTAA
TTAAACATAACCATAGCATAAGGATAATCGGGCACACGATTATTATTACCTTGTTGGTGGCGAGTGCCACCCATACCTGTGCGGTTTGTGCGTAGGTGAC[G/A]
TCGTAGCTGTGCTTGCCTTGTAGCTGGTGTGTCAATATAGCCACTGGAATCATACACCGTATCTTCCGGATGAGCATCGTCGTCACCACTCACCACTTCC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 80.20% | 9.30% | 6.05% | 4.51% | NA |
| All Indica | 2759 | 75.10% | 8.30% | 9.79% | 6.78% | NA |
| All Japonica | 1512 | 98.30% | 0.10% | 0.20% | 1.46% | NA |
| Aus | 269 | 24.50% | 71.70% | 2.60% | 1.12% | NA |
| Indica I | 595 | 79.50% | 8.20% | 7.06% | 5.21% | NA |
| Indica II | 465 | 79.60% | 2.40% | 12.04% | 6.02% | NA |
| Indica III | 913 | 66.20% | 11.70% | 13.25% | 8.87% | NA |
| Indica Intermediate | 786 | 79.60% | 7.90% | 6.49% | 5.98% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 95.80% | 0.20% | 0.20% | 3.77% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 90.60% | 8.30% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 7.80% | 5.56% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1112990301 | C -> T | LOC_Os11g22580.1 | missense_variant ; p.Arg257Cys; MODERATE | nonsynonymous_codon ; R257C | Average:12.211; most accessible tissue: Callus, score: 42.321 | unknown | unknown | TOLERATED | 0.11 |
| vg1112990301 | C -> DEL | LOC_Os11g22580.1 | N | frameshift_variant | Average:12.211; most accessible tissue: Callus, score: 42.321 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1112990301 | NA | 9.58E-19 | mr1119 | 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 |
| vg1112990301 | NA | 1.27E-13 | mr1166 | 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 |
| vg1112990301 | NA | 5.49E-09 | mr1275 | 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 |
| vg1112990301 | 5.31E-07 | 5.31E-07 | mr1275 | 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 |
| vg1112990301 | NA | 6.42E-06 | mr1393 | 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 |
| vg1112990301 | NA | 9.43E-06 | mr1434 | 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 |