| Variant ID: vg1212529629 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12529629 |
| 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: 0.03, others allele: 0.00, population size: 250. )
GATGTTGCGGGTTTCGCGTTCGTGACGGCATGAAGGCGAAATACATCCCTCTCCAATGCCACACATCCTGGAGCCAATGGAGGTCGAGATGGTTCTACCT[C/T]
GAGCAGAAAGAACTTGACCTGGTTCTTGTCGTGCCCGAGGTCCGACCAGAGCGCTTCGAGGACTGGACCTCTAAACCTCCATTGACGCCCTCTCTCGAAA
TTTCGAGAGAGGGCGTCAATGGAGGTTTAGAGGTCCAGTCCTCGAAGCGCTCTGGTCGGACCTCGGGCACGACAAGAACCAGGTCAAGTTCTTTCTGCTC[G/A]
AGGTAGAACCATCTCGACCTCCATTGGCTCCAGGATGTGTGGCATTGGAGAGGGATGTATTTCGCCTTCATGCCGTCACGAACGCGAAACCCGCAACATC
| 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 | 57.90% | 30.30% | 1.31% | 10.54% | NA |
| All Indica | 2759 | 56.10% | 30.20% | 1.74% | 11.96% | NA |
| All Japonica | 1512 | 56.00% | 34.20% | 0.73% | 9.06% | NA |
| Aus | 269 | 78.80% | 13.40% | 0.37% | 7.43% | NA |
| Indica I | 595 | 61.20% | 28.70% | 1.34% | 8.74% | NA |
| Indica II | 465 | 48.20% | 38.50% | 0.43% | 12.90% | NA |
| Indica III | 913 | 52.40% | 29.70% | 2.52% | 15.44% | NA |
| Indica Intermediate | 786 | 61.50% | 26.80% | 1.91% | 9.80% | NA |
| Temperate Japonica | 767 | 81.20% | 18.50% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 16.50% | 58.30% | 2.18% | 23.02% | NA |
| Japonica Intermediate | 241 | 58.50% | 33.60% | 0.00% | 7.88% | NA |
| VI/Aromatic | 96 | 69.80% | 26.00% | 1.04% | 3.12% | NA |
| Intermediate | 90 | 66.70% | 23.30% | 1.11% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212529629 | C -> DEL | LOC_Os12g22230.1 | N | frameshift_variant | Average:70.416; most accessible tissue: Zhenshan97 young leaf, score: 85.184 | N | N | N | N |
| vg1212529629 | C -> T | LOC_Os12g22230.1 | synonymous_variant ; p.Leu155Leu; LOW | synonymous_codon | Average:70.416; most accessible tissue: Zhenshan97 young leaf, score: 85.184 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1212529629 | NA | 4.99E-06 | mr1700 | Jap_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 |
| vg1212529629 | NA | 4.43E-06 | mr1425_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 |
| vg1212529629 | NA | 7.92E-09 | mr1425_2 | 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 |