| Variant ID: vg0206228771 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 6228771 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.00, others allele: 0.00, population size: 245. )
CCCTGTGGGGTAATGCAGCATCCACGCGATCGTGGAGGCTCAAACCATCATTGAATTTTTCATCGGTTGGACGCTTTCCAGTTAATATCTCTAACAACAG[T/C]
ACTCCATAGCTGTAGACATCACCCTTCGTTGATATTTGCCCACCCATTCCGTACTCTGCATTTTCATTTGAAAACATAAGAAAGGTGAATTGTGGAAAAC
GTTTTCCACAATTCACCTTTCTTATGTTTTCAAATGAAAATGCAGAGTACGGAATGGGTGGGCAAATATCAACGAAGGGTGATGTCTACAGCTATGGAGT[A/G]
CTGTTGTTAGAGATATTAACTGGAAAGCGTCCAACCGATGAAAAATTCAATGATGGTTTGAGCCTCCACGATCGCGTGGATGCTGCATTACCCCACAGGG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.10% | 8.10% | 6.43% | 7.32% | NA |
| All Indica | 2759 | 63.20% | 13.60% | 10.84% | 12.29% | NA |
| All Japonica | 1512 | 99.50% | 0.10% | 0.13% | 0.26% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.74% | 0.00% | NA |
| Indica I | 595 | 51.10% | 4.90% | 21.34% | 22.69% | NA |
| Indica II | 465 | 52.30% | 27.30% | 8.60% | 11.83% | NA |
| Indica III | 913 | 70.80% | 15.10% | 6.68% | 7.45% | NA |
| Indica Intermediate | 786 | 70.20% | 10.40% | 9.03% | 10.31% | NA |
| Temperate Japonica | 767 | 99.20% | 0.30% | 0.26% | 0.26% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 92.20% | 4.40% | 1.11% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0206228771 | T -> DEL | LOC_Os02g12010.1 | N | frameshift_variant | Average:20.75; most accessible tissue: Callus, score: 65.442 | N | N | N | N |
| vg0206228771 | T -> C | LOC_Os02g12010.1 | synonymous_variant ; p.Val940Val; LOW | synonymous_codon | Average:20.75; most accessible tissue: Callus, score: 65.442 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0206228771 | NA | 4.70E-08 | mr1170 | 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 |
| vg0206228771 | 8.02E-07 | NA | mr1170_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 |
| vg0206228771 | 8.78E-06 | 8.32E-08 | mr1170_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 |