| Variant ID: vg0209218990 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9218990 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.63, G: 0.34, C: 0.01, others allele: 0.00, population size: 76. )
AAATGGCGTAGATGATCCACATGCGCAGGTACTTGTCATCTGCTAACTTCAACTTCTCCAATTGAATCCCAAGAGAAGTCAGTGATGGTGAGATACCATC[A/G]
TTGATTCCAAGCAAATTCAGCACAAATTCTGTAGCTTCAGATTCCATCTCATATGAGACATCCTTGTCGCCCATTGGGATACCAAGTACAGACTTCACTG
CAGTGAAGTCTGTACTTGGTATCCCAATGGGCGACAAGGATGTCTCATATGAGATGGAATCTGAAGCTACAGAATTTGTGCTGAATTTGCTTGGAATCAA[T/C]
GATGGTATCTCACCATCACTGACTTCTCTTGGGATTCAATTGGAGAAGTTGAAGTTAGCAGATGACAAGTACCTGCGCATGTGGATCATCTACGCCATTT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 49.40% | 40.80% | 3.68% | 6.03% | NA |
| All Indica | 2759 | 24.70% | 65.20% | 5.18% | 4.93% | NA |
| All Japonica | 1512 | 97.30% | 1.20% | 0.53% | 0.99% | NA |
| Aus | 269 | 15.20% | 31.20% | 6.32% | 47.21% | NA |
| Indica I | 595 | 50.90% | 38.30% | 4.03% | 6.72% | NA |
| Indica II | 465 | 18.30% | 71.20% | 6.45% | 4.09% | NA |
| Indica III | 913 | 10.30% | 82.90% | 4.71% | 2.08% | NA |
| Indica Intermediate | 786 | 25.40% | 61.30% | 5.85% | 7.38% | NA |
| Temperate Japonica | 767 | 98.20% | 0.80% | 0.00% | 1.04% | NA |
| Tropical Japonica | 504 | 96.00% | 1.40% | 1.59% | 0.99% | NA |
| Japonica Intermediate | 241 | 97.10% | 2.10% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 88.50% | 9.40% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 64.40% | 23.30% | 4.44% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0209218990 | A -> G | LOC_Os02g16220.1 | synonymous_variant ; p.Asn284Asn; LOW | synonymous_codon | Average:16.469; most accessible tissue: Callus, score: 39.762 | N | N | N | N |
| vg0209218990 | A -> DEL | LOC_Os02g16220.1 | N | frameshift_variant | Average:16.469; most accessible tissue: Callus, score: 39.762 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0209218990 | 1.82E-06 | 2.58E-07 | mr1304 | 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 |
| vg0209218990 | NA | 2.49E-06 | mr1201_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 |