| Variant ID: vg0508237720 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 8237720 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.70, G: 0.29, others allele: 0.00, population size: 209. )
CCTTCCAACCCGGCGCGTGATTCTTCGCTGCAATAGTCGTGGGGACCTCTACACTCTACCTACTACTGTCCCTGCCATCACCGCCCACAGCTTCCTCGCC[A/G]
AGTCATCCACCTTATGGCATCATCGCCTTGGTCACCCCAGTCCAGCCGCAGTCCAAACTCTTCATAAATTAGCTATTCTTTCTTGTACTAGGTCTAATAA
TTATTAGACCTAGTACAAGAAAGAATAGCTAATTTATGAAGAGTTTGGACTGCGGCTGGACTGGGGTGACCAAGGCGATGATGCCATAAGGTGGATGACT[T/C]
GGCGAGGAAGCTGTGGGCGGTGATGGCAGGGACAGTAGTAGGTAGAGTGTAGAGGTCCCCACGACTATTGCAGCGAAGAATCACGCGCCGGGTTGGAAGG
| 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 | 56.60% | 43.00% | 0.06% | 0.34% | NA |
| All Indica | 2759 | 35.30% | 64.20% | 0.11% | 0.47% | NA |
| All Japonica | 1512 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 20.40% | 79.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 41.20% | 58.30% | 0.00% | 0.50% | NA |
| Indica II | 465 | 55.50% | 43.90% | 0.43% | 0.22% | NA |
| Indica III | 913 | 25.30% | 74.20% | 0.00% | 0.55% | NA |
| Indica Intermediate | 786 | 30.40% | 69.00% | 0.13% | 0.51% | NA |
| Temperate Japonica | 767 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 60.00% | 36.70% | 0.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0508237720 | A -> DEL | N | N | silent_mutation | Average:47.926; most accessible tissue: Zhenshan97 young leaf, score: 63.653 | N | N | N | N |
| vg0508237720 | A -> G | LOC_Os05g14520-LOC_Os05g14540 | intergenic_region ; MODIFIER | silent_mutation | Average:47.926; most accessible tissue: Zhenshan97 young leaf, score: 63.653 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0508237720 | NA | 6.04E-11 | mr1593 | 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 |
| vg0508237720 | NA | 1.18E-19 | mr1195_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 |
| vg0508237720 | 7.16E-06 | 2.12E-15 | mr1593_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 |