| Variant ID: vg0212545067 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 12545067 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 116. )
GTGCGTCCTTGAAGAAATTGTAGGAGGAGGGCACTCTCCCCAGTCATGGGACTATGGAGAGGGAACCGGGAGGTACTGAACCTGAACCCGTCCTGGGCCG[C/T]
ATGGTTGCGGTTGAGGACTACATTCTCTGTGGTTTTCTTCCTCCGCCTTCTGAGTTTTTCCTTCTTGTATTGAACTTCTACGGTCTTTCTCTGCTCCATC
GATGGAGCAGAGAAAGACCGTAGAAGTTCAATACAAGAAGGAAAAACTCAGAAGGCGGAGGAAGAAAACCACAGAGAATGTAGTCCTCAACCGCAACCAT[G/A]
CGGCCCAGGACGGGTTCAGGTTCAGTACCTCCCGGTTCCCTCTCCATAGTCCCATGACTGGGGAGAGTGCCCTCCTCCTACAATTTCTTCAAGGACGCAC
| 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 | 61.80% | 37.90% | 0.28% | 0.00% | NA |
| All Indica | 2759 | 96.30% | 3.40% | 0.25% | 0.00% | NA |
| All Japonica | 1512 | 1.70% | 98.30% | 0.07% | 0.00% | NA |
| Aus | 269 | 71.00% | 28.60% | 0.37% | 0.00% | NA |
| Indica I | 595 | 98.70% | 1.20% | 0.17% | 0.00% | NA |
| Indica II | 465 | 97.00% | 2.60% | 0.43% | 0.00% | NA |
| Indica III | 913 | 97.30% | 2.60% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 93.00% | 6.60% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 2.40% | 97.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.10% | 97.50% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 8.30% | 91.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 44.40% | 51.10% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0212545067 | C -> T | LOC_Os02g21130.1 | synonymous_variant ; p.Arg16Arg; LOW | synonymous_codon | Average:32.309; most accessible tissue: Zhenshan97 flag leaf, score: 49.845 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0212545067 | 1.63E-06 | NA | mr1531 | 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 |
| vg0212545067 | 8.20E-06 | NA | mr1531 | 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 |
| vg0212545067 | NA | 8.46E-06 | mr1992_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 |