| Variant ID: vg1000239938 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 239938 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 281. )
TCTCTCCGTCGGGACCATGTCGTTGTTGTTCCTACTATTTTGGTTTTCTTCATTGCTCTTCCCAGTGCCCCTCTTCTCCCCTGCATTCCCTCCCTCTTGC[G/A]
CGTTCAAAGAAAACAGAACCCCCTCGTCTGAGAACGCGTTTTGATGCACTCACCCGCCCGGGTTCACCACCAGAGTTCGTCATTGTCGTTTCTCTCTCCG
CGGAGAGAGAAACGACAATGACGAACTCTGGTGGTGAACCCGGGCGGGTGAGTGCATCAAAACGCGTTCTCAGACGAGGGGGTTCTGTTTTCTTTGAACG[C/T]
GCAAGAGGGAGGGAATGCAGGGGAGAAGAGGGGCACTGGGAAGAGCAATGAAGAAAACCAAAATAGTAGGAACAACAACGACATGGTCCCGACGGAGAGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.60% | 4.70% | 0.70% | 16.00% | NA |
| All Indica | 2759 | 90.40% | 7.80% | 0.72% | 1.12% | NA |
| All Japonica | 1512 | 64.20% | 0.10% | 0.07% | 35.65% | NA |
| Aus | 269 | 53.90% | 0.00% | 2.60% | 43.49% | NA |
| Indica I | 595 | 98.30% | 0.70% | 1.01% | 0.00% | NA |
| Indica II | 465 | 96.80% | 1.30% | 0.65% | 1.29% | NA |
| Indica III | 913 | 86.10% | 13.30% | 0.33% | 0.33% | NA |
| Indica Intermediate | 786 | 85.50% | 10.70% | 1.02% | 2.80% | NA |
| Temperate Japonica | 767 | 89.70% | 0.00% | 0.13% | 10.17% | NA |
| Tropical Japonica | 504 | 27.20% | 0.40% | 0.00% | 72.42% | NA |
| Japonica Intermediate | 241 | 60.20% | 0.00% | 0.00% | 39.83% | NA |
| VI/Aromatic | 96 | 42.70% | 0.00% | 3.12% | 54.17% | NA |
| Intermediate | 90 | 73.30% | 5.60% | 2.22% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000239938 | G -> A | LOC_Os10g01400.1 | upstream_gene_variant ; 3600.0bp to feature; MODIFIER | silent_mutation | Average:22.414; most accessible tissue: Zhenshan97 young leaf, score: 32.0 | N | N | N | N |
| vg1000239938 | G -> A | LOC_Os10g01390.1 | intron_variant ; MODIFIER | silent_mutation | Average:22.414; most accessible tissue: Zhenshan97 young leaf, score: 32.0 | N | N | N | N |
| vg1000239938 | G -> DEL | N | N | silent_mutation | Average:22.414; most accessible tissue: Zhenshan97 young leaf, score: 32.0 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000239938 | 3.46E-07 | 3.46E-07 | mr1260 | 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 |
| vg1000239938 | NA | 4.58E-06 | mr1613 | 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 |
| vg1000239938 | NA | 6.56E-06 | mr1559_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 |
| vg1000239938 | NA | 4.10E-06 | mr1795_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 |
| vg1000239938 | NA | 6.84E-07 | mr1888_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 |