| Variant ID: vg0708363931 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 8363931 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.60, C: 0.40, others allele: 0.00, population size: 77. )
ATCACGCCCACCCTCGCCACCGGTGCTTAGGAAAGGGTCGAGCTATACTTCAGATCAAGCAGTTACCCACTCCCGCTTGTGGTAAGCATGGTAAGTCTCC[T/C]
AGGGTTTCTCATGAACCGGTCCTTAATTGCCATGGGTGCGACCAGCAAAACCATGCACCCACAGCCCACCATTTAGTGTATTTTAATTAACTAACACCAT
ATGGTGTTAGTTAATTAAAATACACTAAATGGTGGGCTGTGGGTGCATGGTTTTGCTGGTCGCACCCATGGCAATTAAGGACCGGTTCATGAGAAACCCT[A/G]
GGAGACTTACCATGCTTACCACAAGCGGGAGTGGGTAACTGCTTGATCTGAAGTATAGCTCGACCCTTTCCTAAGCACCGGTGGCGAGGGTGGGCGTGAT
| 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 | 37.00% | 9.50% | 13.67% | 39.84% | NA |
| All Indica | 2759 | 5.30% | 6.00% | 22.62% | 66.11% | NA |
| All Japonica | 1512 | 87.20% | 11.80% | 0.13% | 0.86% | NA |
| Aus | 269 | 60.60% | 34.90% | 0.74% | 3.72% | NA |
| Indica I | 595 | 3.50% | 2.00% | 16.64% | 77.82% | NA |
| Indica II | 465 | 6.70% | 1.30% | 15.05% | 76.99% | NA |
| Indica III | 913 | 4.60% | 9.30% | 29.03% | 57.06% | NA |
| Indica Intermediate | 786 | 6.60% | 7.90% | 24.17% | 61.32% | NA |
| Temperate Japonica | 767 | 83.60% | 15.40% | 0.00% | 1.04% | NA |
| Tropical Japonica | 504 | 88.70% | 10.90% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 95.40% | 2.50% | 0.41% | 1.66% | NA |
| VI/Aromatic | 96 | 79.20% | 1.00% | 11.46% | 8.33% | NA |
| Intermediate | 90 | 50.00% | 11.10% | 7.78% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0708363931 | T -> DEL | N | N | silent_mutation | Average:35.505; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0708363931 | T -> C | LOC_Os07g14660.1 | upstream_gene_variant ; 4726.0bp to feature; MODIFIER | silent_mutation | Average:35.505; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0708363931 | T -> C | LOC_Os07g14670.1 | upstream_gene_variant ; 2495.0bp to feature; MODIFIER | silent_mutation | Average:35.505; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0708363931 | T -> C | LOC_Os07g14680.1 | intron_variant ; MODIFIER | silent_mutation | Average:35.505; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0708363931 | NA | 1.81E-08 | mr1827 | 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 |
| vg0708363931 | 8.96E-06 | NA | mr1242_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 |
| vg0708363931 | NA | 7.09E-06 | mr1243_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 |
| vg0708363931 | 2.94E-06 | NA | mr1496_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 |