| Variant ID: vg0320046683 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 20046683 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 43. )
TGGGCCGGGGTCCCAAACAAAGTTACAAGCCCAAAGGCCCATGACTGGTGATGCAACACCTTGTTTCTTCATTTGTGGACGACTGGGATGGAATTTGGAG[T/G]
TGAGGCCGGATCCGCTGGAAAGAGGACTCCAAGAGCTTTCCACCAAGTACTCACGGGTCAAAAACGGAGGTTGTATGCAGATTCGGCGGCTGATTGAATT
AATTCAATCAGCCGCCGAATCTGCATACAACCTCCGTTTTTGACCCGTGAGTACTTGGTGGAAAGCTCTTGGAGTCCTCTTTCCAGCGGATCCGGCCTCA[A/C]
CTCCAAATTCCATCCCAGTCGTCCACAAATGAAGAAACAAGGTGTTGCATCACCAGTCATGGGCCTTTGGGCTTGTAACTTTGTTTGGGACCCCGGCCCA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.90% | 8.70% | 6.07% | 52.37% | NA |
| All Indica | 2759 | 3.70% | 14.50% | 9.24% | 72.49% | NA |
| All Japonica | 1512 | 86.10% | 0.00% | 0.26% | 13.62% | NA |
| Aus | 269 | 11.90% | 2.60% | 8.18% | 77.32% | NA |
| Indica I | 595 | 3.00% | 14.60% | 8.07% | 74.29% | NA |
| Indica II | 465 | 4.50% | 7.30% | 5.81% | 82.37% | NA |
| Indica III | 913 | 2.40% | 19.20% | 11.72% | 66.70% | NA |
| Indica Intermediate | 786 | 5.30% | 13.40% | 9.29% | 72.01% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 66.50% | 0.00% | 0.60% | 32.94% | NA |
| Japonica Intermediate | 241 | 84.20% | 0.00% | 0.41% | 15.35% | NA |
| VI/Aromatic | 96 | 72.90% | 0.00% | 1.04% | 26.04% | NA |
| Intermediate | 90 | 53.30% | 1.10% | 5.56% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0320046683 | T -> DEL | N | N | silent_mutation | Average:12.031; most accessible tissue: Callus, score: 34.336 | N | N | N | N |
| vg0320046683 | T -> G | LOC_Os03g36130.1 | 5_prime_UTR_variant ; 1966.0bp to feature; MODIFIER | silent_mutation | Average:12.031; most accessible tissue: Callus, score: 34.336 | N | N | N | N |
| vg0320046683 | T -> G | LOC_Os03g36140.1 | downstream_gene_variant ; 2556.0bp to feature; MODIFIER | silent_mutation | Average:12.031; most accessible tissue: Callus, score: 34.336 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0320046683 | NA | 3.32E-08 | mr1718 | 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 |
| vg0320046683 | 5.80E-07 | NA | mr1750 | 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 |
| vg0320046683 | 2.30E-09 | 5.55E-15 | mr1750 | 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 |
| vg0320046683 | 1.44E-06 | 1.44E-06 | mr1987 | 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 |
| vg0320046683 | NA | 1.18E-12 | mr1770_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 |