| Variant ID: vg0118433273 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 18433273 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.72, A: 0.26, others allele: 0.00, population size: 76. )
TCCCTTATTCCGCATTTTGCAGAGTCTTTTTGGTCTTTGCTCCGCGGAGGCCAAAAAGAACCGCCGATTGCGGAATTCGGCAAAGAAAACAGCTCGCGAC[A/G]
TCAAGTTCCTCAAGGCAAGGTATTATGAGGACCACCACATTGATGTCCCTCCTCCTCCGGGTTTCAAGGCCGAGCCCGATGAGCCAGAGGACGAAGAGAT
ATCTCTTCGTCCTCTGGCTCATCGGGCTCGGCCTTGAAACCCGGAGGAGGAGGGACATCAATGTGGTGGTCCTCATAATACCTTGCCTTGAGGAACTTGA[T/C]
GTCGCGAGCTGTTTTCTTTGCCGAATTCCGCAATCGGCGGTTCTTTTTGGCCTCCGCGGAGCAAAGACCAAAAAGACTCTGCAAAATGCGGAATAAGGGA
| 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 | 41.40% | 26.80% | 3.26% | 28.59% | NA |
| All Indica | 2759 | 8.50% | 42.80% | 4.46% | 44.18% | NA |
| All Japonica | 1512 | 94.70% | 1.70% | 1.79% | 1.79% | NA |
| Aus | 269 | 53.50% | 11.20% | 0.74% | 34.57% | NA |
| Indica I | 595 | 1.20% | 50.40% | 2.02% | 46.39% | NA |
| Indica II | 465 | 15.70% | 67.10% | 4.52% | 12.69% | NA |
| Indica III | 913 | 9.10% | 17.40% | 7.56% | 65.94% | NA |
| Indica Intermediate | 786 | 9.20% | 52.30% | 2.67% | 35.88% | NA |
| Temperate Japonica | 767 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 88.30% | 1.60% | 5.36% | 4.76% | NA |
| Japonica Intermediate | 241 | 93.40% | 5.40% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 1.04% | 2.08% | NA |
| Intermediate | 90 | 56.70% | 31.10% | 1.11% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0118433273 | A -> G | LOC_Os01g33470.1 | synonymous_variant ; p.Thr417Thr; LOW | synonymous_codon | Average:47.705; most accessible tissue: Minghui63 flag leaf, score: 81.052 | N | N | N | N |
| vg0118433273 | A -> DEL | LOC_Os01g33470.1 | N | frameshift_variant | Average:47.705; most accessible tissue: Minghui63 flag leaf, score: 81.052 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0118433273 | NA | 2.93E-08 | mr1559 | 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 |
| vg0118433273 | NA | 9.30E-06 | mr1105_2 | 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 |
| vg0118433273 | NA | 8.98E-06 | mr1169_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 |
| vg0118433273 | NA | 1.67E-06 | mr1275_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 |
| vg0118433273 | NA | 8.87E-06 | mr1405_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 |