| Variant ID: vg0714252145 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14252145 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 281. )
AGCAAGCAAACTAACACAACGATCTAAGGCAATGACTTAGCACAACGGTCTAGGTCTTCCGGGCATCGGAGTTGATTGAAGGCTCGTTCGGCACGTCCCC[A/G]
TCATCTTGAGTTGGTCCCCACTCGATCTTGGAATGGGTGCGCTTGGATTCCTCTTCATCATCATCACTTACATTGACGACCGGAGGATCCGCTGGGGCTA
TAGCCCCAGCGGATCCTCCGGTCGTCAATGTAAGTGATGATGATGAAGAGGAATCCAAGCGCACCCATTCCAAGATCGAGTGGGGACCAACTCAAGATGA[T/C]
GGGGACGTGCCGAACGAGCCTTCAATCAACTCCGATGCCCGGAAGACCTAGACCGTTGTGCTAAGTCATTGCCTTAGATCGTTGTGTTAGTTTGCTTGCT
| 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 | 87.60% | 0.90% | 2.64% | 8.89% | NA |
| All Indica | 2759 | 85.60% | 1.40% | 4.28% | 8.70% | NA |
| All Japonica | 1512 | 88.20% | 0.10% | 0.40% | 11.24% | NA |
| Aus | 269 | 98.50% | 0.40% | 0.00% | 1.12% | NA |
| Indica I | 595 | 91.40% | 0.70% | 3.03% | 4.87% | NA |
| Indica II | 465 | 89.70% | 1.50% | 4.30% | 4.52% | NA |
| Indica III | 913 | 75.80% | 2.30% | 5.59% | 16.32% | NA |
| Indica Intermediate | 786 | 90.30% | 0.80% | 3.69% | 5.22% | NA |
| Temperate Japonica | 767 | 87.50% | 0.00% | 0.13% | 12.39% | NA |
| Tropical Japonica | 504 | 89.70% | 0.40% | 0.79% | 9.13% | NA |
| Japonica Intermediate | 241 | 87.60% | 0.00% | 0.41% | 12.03% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 92.20% | 1.10% | 1.11% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0714252145 | A -> DEL | N | N | silent_mutation | Average:17.614; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg0714252145 | A -> G | LOC_Os07g25010.1 | intron_variant ; MODIFIER | silent_mutation | Average:17.614; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714252145 | NA | 3.23E-07 | mr1709 | 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 |
| vg0714252145 | NA | 4.16E-06 | mr1963 | 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 |