| Variant ID: vg0910500550 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10500550 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 78. )
GGAGCCGCACCTCGCCGCCGCGGCGTGCCGCCTGTGCCCCGGCTGGGTCGAGCATAGCGAGAGGAGGAAGAAGAGAAGCCGAGCCGAGCCACTGCCAAGC[C/T]
GGTCCCACCTCCCTTTCCTCTCTCCTGTCACTGATAGCCGGGCCCCGCACCTCCCTCTATCCCTCAAGCAGCAGACAAGCCTGGGCCCGCGCATCATTCC
GGAATGATGCGCGGGCCCAGGCTTGTCTGCTGCTTGAGGGATAGAGGGAGGTGCGGGGCCCGGCTATCAGTGACAGGAGAGAGGAAAGGGAGGTGGGACC[G/A]
GCTTGGCAGTGGCTCGGCTCGGCTTCTCTTCTTCCTCCTCTCGCTATGCTCGACCCAGCCGGGGCACAGGCGGCACGCCGCGGCGGCGAGGTGCGGCTCC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.90% | 43.00% | 0.49% | 0.59% | NA |
| All Indica | 2759 | 31.20% | 67.80% | 0.72% | 0.25% | NA |
| All Japonica | 1512 | 92.80% | 5.80% | 0.07% | 1.39% | NA |
| Aus | 269 | 85.50% | 14.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 63.70% | 36.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 24.30% | 73.50% | 1.72% | 0.43% | NA |
| Indica III | 913 | 17.60% | 81.70% | 0.44% | 0.22% | NA |
| Indica Intermediate | 786 | 26.60% | 72.30% | 0.76% | 0.38% | NA |
| Temperate Japonica | 767 | 95.40% | 4.40% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 88.50% | 7.30% | 0.00% | 4.17% | NA |
| Japonica Intermediate | 241 | 93.40% | 6.60% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 62.20% | 35.60% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910500550 | C -> DEL | N | N | silent_mutation | Average:65.144; most accessible tissue: Zhenshan97 panicle, score: 74.671 | N | N | N | N |
| vg0910500550 | C -> T | LOC_Os09g17130.1 | upstream_gene_variant ; 4556.0bp to feature; MODIFIER | silent_mutation | Average:65.144; most accessible tissue: Zhenshan97 panicle, score: 74.671 | N | N | N | N |
| vg0910500550 | C -> T | LOC_Os09g17130-LOC_Os09g17140 | intergenic_region ; MODIFIER | silent_mutation | Average:65.144; most accessible tissue: Zhenshan97 panicle, score: 74.671 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0910500550 | NA | 3.93E-13 | mr1170 | 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 |
| vg0910500550 | NA | 1.47E-08 | mr1170 | 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 |
| vg0910500550 | 3.57E-06 | 1.98E-07 | mr1627 | Jap_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 |
| vg0910500550 | NA | 1.68E-06 | mr1984 | 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 |
| vg0910500550 | NA | 5.79E-06 | mr1170_2 | 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 |