| Variant ID: vg0334753499 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34753499 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 318. )
TTAAAACATAATCCTTGTGCTCTCCGGTACTCTTTCAACTGCTGAGCCTTCCACAATTCACCAGGAGCCAACTTCTGTTTCTCTCCACCTCGTCCCACCT[G/A]
AAAGTTCTTCTTAGAAACAGATTTCTTACTCCCAGAACTAGGCAAAGCACTCTCATAAGCTAGAGCCACTAAGAAAGCTTGTGTGACTGAAGTGGGTTGT
ACAACCCACTTCAGTCACACAAGCTTTCTTAGTGGCTCTAGCTTATGAGAGTGCTTTGCCTAGTTCTGGGAGTAAGAAATCTGTTTCTAAGAAGAACTTT[C/T]
AGGTGGGACGAGGTGGAGAGAAACAGAAGTTGGCTCCTGGTGAATTGTGGAAGGCTCAGCAGTTGAAAGAGTACCGGAGAGCACAAGGATTATGTTTTAA
| 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 | 93.80% | 3.50% | 2.22% | 0.44% | NA |
| All Indica | 2759 | 91.70% | 4.00% | 3.59% | 0.76% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 79.20% | 19.70% | 1.12% | 0.00% | NA |
| Indica I | 595 | 69.60% | 14.60% | 13.11% | 2.69% | NA |
| Indica II | 465 | 98.50% | 0.00% | 1.51% | 0.00% | NA |
| Indica III | 913 | 99.10% | 0.70% | 0.11% | 0.11% | NA |
| Indica Intermediate | 786 | 95.80% | 2.00% | 1.65% | 0.51% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 3.30% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334753499 | G -> A | LOC_Os03g61190.1 | stop_gained ; p.Gln315*; HIGH | stop_gained | Average:64.737; most accessible tissue: Zhenshan97 young leaf, score: 82.539 | N | N | N | N |
| vg0334753499 | G -> DEL | LOC_Os03g61190.1 | N | frameshift_variant | Average:64.737; most accessible tissue: Zhenshan97 young leaf, score: 82.539 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0334753499 | 3.44E-06 | NA | mr1151 | 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 |
| vg0334753499 | NA | 7.00E-06 | mr1585 | 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 |