| Variant ID: vg0810439839 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 10439839 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, T: 0.20, others allele: 0.00, population size: 218. )
GAGGCATTTAACCAATACTGGGATGTTAGGAAGCTTCCATTGCAAGTGACAGTGAGTGAGCCTTGTTCCCAAATTGTGTCTTGTGTGGATGAAGCTAAAA[C/T]
AGTGGTTCCACTGAGTATGGTTTTACCCACACAAGCAAGTCAGGCTGACAATGTTCCTACCAGAGATGCTACCACAAAAAAGGTTCCCACCAAAAAAAAA
TTTTTTTTTGGTGGGAACCTTTTTTGTGGTAGCATCTCTGGTAGGAACATTGTCAGCCTGACTTGCTTGTGTGGGTAAAACCATACTCAGTGGAACCACT[G/A]
TTTTAGCTTCATCCACACAAGACACAATTTGGGAACAAGGCTCACTCACTGTCACTTGCAATGGAAGCTTCCTAACATCCCAGTATTGGTTAAATGCCTC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.80% | 23.40% | 3.36% | 9.48% | NA |
| All Indica | 2759 | 94.00% | 3.20% | 2.79% | 0.00% | NA |
| All Japonica | 1512 | 6.70% | 64.60% | 4.03% | 24.67% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
| Indica II | 465 | 95.30% | 4.30% | 0.43% | 0.00% | NA |
| Indica III | 913 | 90.40% | 2.30% | 7.34% | 0.00% | NA |
| Indica Intermediate | 786 | 95.80% | 3.20% | 1.02% | 0.00% | NA |
| Temperate Japonica | 767 | 4.60% | 93.20% | 0.39% | 1.83% | NA |
| Tropical Japonica | 504 | 7.10% | 34.30% | 9.52% | 49.01% | NA |
| Japonica Intermediate | 241 | 12.40% | 36.90% | 4.15% | 46.47% | NA |
| VI/Aromatic | 96 | 12.50% | 7.30% | 18.75% | 61.46% | NA |
| Intermediate | 90 | 45.60% | 33.30% | 3.33% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0810439839 | C -> T | LOC_Os08g17050.1 | downstream_gene_variant ; 3087.0bp to feature; MODIFIER | silent_mutation | Average:44.181; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | N | N | N | N |
| vg0810439839 | C -> T | LOC_Os08g17060.1 | downstream_gene_variant ; 4510.0bp to feature; MODIFIER | silent_mutation | Average:44.181; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | N | N | N | N |
| vg0810439839 | C -> T | LOC_Os08g17040.1 | intron_variant ; MODIFIER | silent_mutation | Average:44.181; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | N | N | N | N |
| vg0810439839 | C -> DEL | N | N | silent_mutation | Average:44.181; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0810439839 | NA | 2.39E-08 | mr1595 | 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 |
| vg0810439839 | 5.48E-06 | 6.14E-06 | mr1720_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 |
| vg0810439839 | NA | 3.42E-11 | mr1986_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 |
| vg0810439839 | 1.54E-06 | 5.36E-07 | mr1986_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 |