| Variant ID: vg1217497177 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 17497177 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 186. )
TCCGTCAGGGCCTGGGGCTCTATCAAGAGGCATGTTCTTGATGATATTATTCATTTCTTCCTCAGATGGAATGGATGTCAAATGGTTTAGATCAGTGTCT[G/A]
TATGTAGCAAGCCATTCAGGTTGAGATGATTTTCTGACAAAACAGCAGTGCCCATTCTCTGAAAATAGGTATTGAACTGGGCCTGAGCTTTTTCTTCATG
CATGAAGAAAAAGCTCAGGCCCAGTTCAATACCTATTTTCAGAGAATGGGCACTGCTGTTTTGTCAGAAAATCATCTCAACCTGAATGGCTTGCTACATA[C/T]
AGACACTGATCTAAACCATTTGACATCCATTCCATCTGAGGAAGAAATGAATAATATCATCAAGAACATGCCTCTTGATAGAGCCCCAGGCCCTGACGGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 68.20% | 25.10% | 1.04% | 5.69% | NA |
| All Indica | 2759 | 60.10% | 37.10% | 1.63% | 1.20% | NA |
| All Japonica | 1512 | 92.30% | 0.70% | 0.07% | 6.88% | NA |
| Aus | 269 | 25.70% | 25.30% | 1.12% | 47.96% | NA |
| Indica I | 595 | 75.60% | 17.10% | 6.72% | 0.50% | NA |
| Indica II | 465 | 72.50% | 27.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 40.20% | 59.30% | 0.11% | 0.44% | NA |
| Indica Intermediate | 786 | 64.00% | 32.20% | 0.51% | 3.31% | NA |
| Temperate Japonica | 767 | 87.50% | 0.40% | 0.13% | 11.99% | NA |
| Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 93.40% | 1.70% | 0.00% | 4.98% | NA |
| VI/Aromatic | 96 | 37.50% | 61.50% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 73.30% | 24.40% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1217497177 | G -> DEL | LOC_Os12g29450.1 | N | frameshift_variant | Average:64.891; most accessible tissue: Callus, score: 75.005 | N | N | N | N |
| vg1217497177 | G -> A | LOC_Os12g29450.1 | missense_variant ; p.Thr587Ile; MODERATE | nonsynonymous_codon ; T587I | Average:64.891; most accessible tissue: Callus, score: 75.005 | unknown | unknown | TOLERATED | 0.21 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1217497177 | NA | 4.93E-06 | mr1352 | 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 |
| vg1217497177 | NA | 5.29E-08 | mr1743 | 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 |
| vg1217497177 | NA | 6.42E-06 | mr1092_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 |
| vg1217497177 | NA | 5.24E-07 | mr1220_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 |
| vg1217497177 | NA | 3.16E-07 | mr1743_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 |
| vg1217497177 | NA | 6.22E-06 | mr1968_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 |