| Variant ID: vg1209004311 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9004311 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.60, A: 0.40, others allele: 0.00, population size: 62. )
ATGGTGACTTAGCTTTTTAGTGTTCCCCCGGTAATAGCAGATGTAGCCGATGTGTGGAGAAAGTCGTCCATCAATCCCAATAAAAACACCAGTCGGCGGC[G/A]
ATGGCAGCCGCCGGAAGTGAAGACATGGTCGCCATCAACAACGGCAGCGGATTACACCAACCGTGGAGGCGAAGAAACCGGTCGGCAGTGATGACGGCGG
CCGCCGTCATCACTGCCGACCGGTTTCTTCGCCTCCACGGTTGGTGTAATCCGCTGCCGTTGTTGATGGCGACCATGTCTTCACTTCCGGCGGCTGCCAT[C/T]
GCCGCCGACTGGTGTTTTTATTGGGATTGATGGACGACTTTCTCCACACATCGGCTACATCTGCTATTACCGGGGGAACACTAAAAAGCTAAGTCACCAT
| 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 | 39.60% | 38.20% | 0.40% | 21.88% | NA |
| All Indica | 2759 | 53.70% | 10.50% | 0.65% | 35.16% | NA |
| All Japonica | 1512 | 4.40% | 94.60% | 0.00% | 0.99% | NA |
| Aus | 269 | 81.00% | 5.20% | 0.00% | 13.75% | NA |
| Indica I | 595 | 36.10% | 21.00% | 0.84% | 42.02% | NA |
| Indica II | 465 | 50.80% | 13.80% | 0.43% | 35.05% | NA |
| Indica III | 913 | 65.30% | 2.20% | 0.22% | 32.31% | NA |
| Indica Intermediate | 786 | 55.30% | 10.20% | 1.15% | 33.33% | NA |
| Temperate Japonica | 767 | 6.00% | 93.00% | 0.00% | 1.04% | NA |
| Tropical Japonica | 504 | 3.60% | 95.80% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 1.20% | 97.10% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 72.90% | 22.90% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 36.70% | 53.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1209004311 | G -> DEL | LOC_Os12g15770.1 | N | frameshift_variant | Average:40.717; most accessible tissue: Callus, score: 70.638 | N | N | N | N |
| vg1209004311 | G -> A | LOC_Os12g15770.1 | synonymous_variant ; p.Ile109Ile; LOW | synonymous_codon | Average:40.717; most accessible tissue: Callus, score: 70.638 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1209004311 | NA | 1.91E-08 | mr1425 | 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 |
| vg1209004311 | NA | 6.85E-08 | mr1659 | 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 |
| vg1209004311 | NA | 1.04E-06 | mr1864_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 |