| Variant ID: vg1209054462 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9054462 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.73, G: 0.25, others allele: 0.00, population size: 68. )
ACAACGGCTCCCAGTTCATCAGTGCCGACTTCCAGGATGACTGCATCGGGCTGGGAGAGTCAAAATATGCTTCACTTCGGTTTCCCATCCTCAAAGCAAC[A/G]
GACAAGTCGAGAGGGCAAACGGCATAGTACTACAAGGGATCAAGACCCGTGTCTACGACAGGCTCATGTCACATGACAACAAATGGGTCGAAGAACTCCC
GGGAGTTCTTCGACCCATTTGTTGTCATGTGACATGAGCCTGTCGTAGACACGGGTCTTGATCCCTTGTAGTACTATGCCGTTTGCCCTCTCGACTTGTC[T/C]
GTTGCTTTGAGGATGGGAAACCGAAGTGAAGCATATTTTGACTCTCCCAGCCCGATGCAGTCATCCTGGAAGTCGGCACTGATGAACTGGGAGCCGTTGT
| 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 | 39.40% | 36.30% | 2.73% | 21.60% | NA |
| All Indica | 2759 | 53.40% | 7.40% | 3.91% | 35.30% | NA |
| All Japonica | 1512 | 4.20% | 94.40% | 0.00% | 1.39% | NA |
| Aus | 269 | 83.30% | 3.70% | 6.69% | 6.32% | NA |
| Indica I | 595 | 35.10% | 10.80% | 2.35% | 51.76% | NA |
| Indica II | 465 | 51.20% | 9.00% | 2.80% | 36.99% | NA |
| Indica III | 913 | 64.60% | 3.20% | 5.04% | 27.16% | NA |
| Indica Intermediate | 786 | 55.60% | 8.70% | 4.45% | 31.30% | NA |
| Temperate Japonica | 767 | 5.70% | 92.60% | 0.00% | 1.69% | NA |
| Tropical Japonica | 504 | 3.40% | 95.80% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 1.20% | 97.10% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 71.90% | 22.90% | 1.04% | 4.17% | NA |
| Intermediate | 90 | 34.40% | 57.80% | 2.22% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209054462 | A -> DEL | LOC_Os12g15900.1 | N | frameshift_variant | Average:17.724; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| vg1209054462 | A -> G | LOC_Os12g15900.1 | missense_variant ; p.Arg745Gly; MODERATE | nonsynonymous_codon ; R745G | Average:17.724; most accessible tissue: Minghui63 panicle, score: 42.799 | unknown | unknown | TOLERATED | 1.00 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1209054462 | NA | 2.17E-07 | mr1066 | 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 |
| vg1209054462 | NA | 2.31E-06 | mr1677 | 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 |
| vg1209054462 | 2.49E-06 | 2.49E-06 | mr1899 | 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 |
| vg1209054462 | NA | 3.84E-08 | mr1576_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 |