| Variant ID: vg0103214478 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 3214478 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.60, A: 0.41, others allele: 0.00, population size: 63. )
ACATGCTACGTGCGTGTGCCTTGGATTTCGAAGGCACTTGGGATCGTTGTTTGCCGTATGCCGAGTTCTCGTACAACAACAGTTATCAGGCCAGCATTCA[A/G]
ATGTCGCCGAATGAGGCAATGTTCGGAAGAAAGTGCCGCACCCCCTTGTGCTGGAATGAGGTGGGCGAAGCCCTGGTATTCGGTCCTGACATACTCAAGT
ACTTGAGTATGTCAGGACCGAATACCAGGGCTTCGCCCACCTCATTCCAGCACAAGGGGGTGCGGCACTTTCTTCCGAACATTGCCTCATTCGGCGACAT[T/C]
TGAATGCTGGCCTGATAACTGTTGTTGTACGAGAACTCGGCATACGGCAAACAACGATCCCAAGTGCCTTCGAAATCCAAGGCACACGCACGTAGCATGT
| 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 | 13.60% | 11.60% | 7.13% | 67.67% | NA |
| All Indica | 2759 | 4.40% | 18.80% | 8.95% | 67.89% | NA |
| All Japonica | 1512 | 14.20% | 1.30% | 1.85% | 82.61% | NA |
| Aus | 269 | 88.50% | 0.00% | 4.09% | 7.43% | NA |
| Indica I | 595 | 2.20% | 7.60% | 2.69% | 87.56% | NA |
| Indica II | 465 | 6.20% | 8.80% | 9.03% | 75.91% | NA |
| Indica III | 913 | 4.80% | 32.40% | 12.71% | 50.05% | NA |
| Indica Intermediate | 786 | 4.50% | 17.30% | 9.29% | 68.96% | NA |
| Temperate Japonica | 767 | 19.90% | 0.80% | 1.30% | 77.97% | NA |
| Tropical Japonica | 504 | 4.00% | 2.60% | 2.58% | 90.87% | NA |
| Japonica Intermediate | 241 | 17.40% | 0.40% | 2.07% | 80.08% | NA |
| VI/Aromatic | 96 | 46.90% | 1.00% | 41.67% | 10.42% | NA |
| Intermediate | 90 | 24.40% | 12.20% | 12.22% | 51.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0103214478 | A -> G | LOC_Os01g06770.1 | synonymous_variant ; p.Gln1593Gln; LOW | synonymous_codon | Average:10.208; most accessible tissue: Callus, score: 16.894 | N | N | N | N |
| vg0103214478 | A -> DEL | LOC_Os01g06770.1 | N | frameshift_variant | Average:10.208; most accessible tissue: Callus, score: 16.894 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0103214478 | 3.87E-06 | 3.87E-06 | mr1327 | Jap_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 |