| Variant ID: vg0327169890 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 27169890 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.56, G: 0.44, others allele: 0.00, population size: 39. )
TGTACTGTCAAAGTAGTATATCCTACCTTAACATTGATTTTAAGTGCCAGGTTTCGGAGATATTGTGTTGGCGGACATTCTGAACATTCCTAGCTAAACA[G/A]
CACTGAGTTATCACACCAAGTTCAGTTTCACAAAGCCGCTTTATCCTTCCTGCAGATATTACAGATGTGAGACAACAGATGGTTAGCAAAAACACTGCCA
TGGCAGTGTTTTTGCTAACCATCTGTTGTCTCACATCTGTAATATCTGCAGGAAGGATAAAGCGGCTTTGTGAAACTGAACTTGGTGTGATAACTCAGTG[C/T]
TGTTTAGCTAGGAATGTTCAGAATGTCCGCCAACACAATATCTCCGAAACCTGGCACTTAAAATCAATGTTAAGGTAGGATATACTACTTTGACAGTACA
| 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 | 46.90% | 41.90% | 4.08% | 7.11% | NA |
| All Indica | 2759 | 22.90% | 59.60% | 6.09% | 11.42% | NA |
| All Japonica | 1512 | 98.80% | 1.00% | 0.07% | 0.13% | NA |
| Aus | 269 | 2.60% | 85.50% | 6.69% | 5.20% | NA |
| Indica I | 595 | 5.50% | 76.60% | 9.75% | 8.07% | NA |
| Indica II | 465 | 11.40% | 69.00% | 6.45% | 13.12% | NA |
| Indica III | 913 | 42.20% | 43.30% | 1.86% | 12.71% | NA |
| Indica Intermediate | 786 | 20.50% | 60.10% | 8.02% | 11.45% | NA |
| Temperate Japonica | 767 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.40% | 1.20% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 97.10% | 2.50% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 42.70% | 54.20% | 2.08% | 1.04% | NA |
| Intermediate | 90 | 46.70% | 44.40% | 4.44% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0327169890 | G -> A | LOC_Os03g47830.1 | synonymous_variant ; p.Cys572Cys; LOW | synonymous_codon | Average:45.065; most accessible tissue: Minghui63 root, score: 65.279 | N | N | N | N |
| vg0327169890 | G -> DEL | LOC_Os03g47830.1 | N | frameshift_variant | Average:45.065; most accessible tissue: Minghui63 root, score: 65.279 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0327169890 | 1.85E-06 | 1.85E-06 | mr1019 | 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 |
| vg0327169890 | NA | 1.57E-13 | mr1874 | 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 |