| Variant ID: vg0905473217 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 5473217 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, A: 0.29, others allele: 0.00, population size: 68. )
TATATGCTAAAGTCTATTAAATTTCCTACAAATGCTTAAGCTGCCATGTGTCATCATATAAACACTCTCAAGTCACCACAGGTCACTCTAATAAAATAAA[A/G]
AAATCTAACCGTCGATTTTTATTTAAATTGGTGGACCCATTAGTTCATTAGTTTTGAATGGTTAGATTTTTATCTTTACGAGGAAACAAAATCTCCCTCC
GGAGGGAGATTTTGTTTCCTCGTAAAGATAAAAATCTAACCATTCAAAACTAATGAACTAATGGGTCCACCAATTTAAATAAAAATCGACGGTTAGATTT[T/C]
TTTATTTTATTAGAGTGACCTGTGGTGACTTGAGAGTGTTTATATGATGACACATGGCAGCTTAAGCATTTGTAGGAAATTTAATAGACTTTAGCATATA
| 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 | 58.00% | 21.60% | 7.70% | 12.76% | NA |
| All Indica | 2759 | 88.80% | 3.00% | 1.81% | 6.42% | NA |
| All Japonica | 1512 | 12.20% | 56.20% | 13.96% | 17.72% | NA |
| Aus | 269 | 19.30% | 23.00% | 17.84% | 39.78% | NA |
| Indica I | 595 | 92.90% | 0.50% | 1.18% | 5.38% | NA |
| Indica II | 465 | 85.80% | 7.50% | 1.08% | 5.59% | NA |
| Indica III | 913 | 92.00% | 2.50% | 1.20% | 4.27% | NA |
| Indica Intermediate | 786 | 83.70% | 2.70% | 3.44% | 10.18% | NA |
| Temperate Japonica | 767 | 19.00% | 49.80% | 21.90% | 9.26% | NA |
| Tropical Japonica | 504 | 1.40% | 78.00% | 6.35% | 14.29% | NA |
| Japonica Intermediate | 241 | 12.90% | 30.70% | 4.56% | 51.87% | NA |
| VI/Aromatic | 96 | 7.30% | 3.10% | 44.79% | 44.79% | NA |
| Intermediate | 90 | 52.20% | 25.60% | 13.33% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0905473217 | A -> G | LOC_Os09g10030.1 | downstream_gene_variant ; 4154.0bp to feature; MODIFIER | silent_mutation | Average:58.369; most accessible tissue: Zhenshan97 young leaf, score: 82.077 | N | N | N | N |
| vg0905473217 | A -> G | LOC_Os09g10054.1 | intron_variant ; MODIFIER | silent_mutation | Average:58.369; most accessible tissue: Zhenshan97 young leaf, score: 82.077 | N | N | N | N |
| vg0905473217 | A -> DEL | N | N | silent_mutation | Average:58.369; most accessible tissue: Zhenshan97 young leaf, score: 82.077 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0905473217 | 3.90E-07 | NA | mr1013 | 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 |
| vg0905473217 | 1.06E-06 | NA | mr1031 | 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 |
| vg0905473217 | 1.10E-06 | NA | mr1056 | 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 |
| vg0905473217 | 9.63E-06 | NA | mr1013_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 |
| vg0905473217 | 3.43E-06 | NA | mr1031_2 | 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 |