| Variant ID: vg1019873752 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 19873752 |
| 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: 117. )
TTGCGCGCTGTGTGTGTATTGTGAAAACCTGGTTGGGACGACGGGGGTCTCTCAACCAGTTCTCTCTAAAGACCTCGGGAACGCCAGAACTCCTCTCGCT[G/A]
CTGATAACGTTACGTTCAGAGCGCATGAGGATGAGAGTTCATGGAACAGGTGCCACTGATGTTAGTAACCGAAAAGCTTTGCCATGACTAAGCTGATGAA
TTCATCAGCTTAGTCATGGCAAAGCTTTTCGGTTACTAACATCAGTGGCACCTGTTCCATGAACTCTCATCCTCATGCGCTCTGAACGTAACGTTATCAG[C/T]
AGCGAGAGGAGTTCTGGCGTTCCCGAGGTCTTTAGAGAGAACTGGTTGAGAGACCCCCGTCGTCCCAACCAGGTTTTCACAATACACACACAGCGCGCAA
| 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 | 78.10% | 5.70% | 6.60% | 9.61% | NA |
| All Indica | 2759 | 82.10% | 7.40% | 7.18% | 3.33% | NA |
| All Japonica | 1512 | 71.60% | 3.20% | 6.88% | 18.25% | NA |
| Aus | 269 | 64.70% | 5.60% | 1.12% | 28.62% | NA |
| Indica I | 595 | 55.30% | 21.20% | 16.81% | 6.72% | NA |
| Indica II | 465 | 91.80% | 1.10% | 3.66% | 3.44% | NA |
| Indica III | 913 | 92.10% | 2.60% | 3.94% | 1.31% | NA |
| Indica Intermediate | 786 | 85.00% | 6.20% | 5.73% | 3.05% | NA |
| Temperate Japonica | 767 | 91.30% | 0.10% | 0.52% | 8.08% | NA |
| Tropical Japonica | 504 | 35.10% | 9.50% | 17.26% | 38.10% | NA |
| Japonica Intermediate | 241 | 85.50% | 0.00% | 5.39% | 9.13% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 4.17% | 4.17% | NA |
| Intermediate | 90 | 87.80% | 3.30% | 3.33% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1019873752 | G -> A | LOC_Os10g37120-LOC_Os10g37160 | intergenic_region ; MODIFIER | silent_mutation | Average:12.143; most accessible tissue: Zhenshan97 flower, score: 24.143 | N | N | N | N |
| vg1019873752 | G -> DEL | N | N | silent_mutation | Average:12.143; most accessible tissue: Zhenshan97 flower, score: 24.143 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1019873752 | NA | 4.54E-06 | mr1274 | 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 |
| vg1019873752 | 1.96E-06 | 7.04E-06 | mr1702 | 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 |
| vg1019873752 | NA | 1.45E-06 | mr1201_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 |
| vg1019873752 | NA | 9.01E-07 | mr1201_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 |
| vg1019873752 | NA | 1.05E-06 | mr1219_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 |