| Variant ID: vg0210599887 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 10599887 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AACTCCATAATGGATTTCCCCAACTTATGCTGAAAACGTCCGCATACGCACAAGCATACCATGTCGATATGTGACGTATATCGAAGGGTAGAGGGTATAC[C/G]
TTTCCCGTAGCCCTGACAGTAGCCCCCGACTTCTGCTTAAATGAACTCGTGAAACCGATTACGACTTCTGATGTCGAAGTTGTCGTCGTTCTCAGTGTGA
TCACACTGAGAACGACGACAACTTCGACATCAGAAGTCGTAATCGGTTTCACGAGTTCATTTAAGCAGAAGTCGGGGGCTACTGTCAGGGCTACGGGAAA[G/C]
GTATACCCTCTACCCTTCGATATACGTCACATATCGACATGGTATGCTTGTGCGTATGCGGACGTTTTCAGCATAAGTTGGGGAAATCCATTATGGAGTT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.70% | 4.60% | 2.50% | 4.19% | NA |
| All Indica | 2759 | 81.30% | 7.80% | 4.02% | 6.92% | NA |
| All Japonica | 1512 | 99.20% | 0.30% | 0.33% | 0.20% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 92.40% | 2.90% | 4.03% | 0.67% | NA |
| Indica II | 465 | 78.70% | 2.60% | 2.80% | 15.91% | NA |
| Indica III | 913 | 72.40% | 15.30% | 5.37% | 6.90% | NA |
| Indica Intermediate | 786 | 84.70% | 5.70% | 3.18% | 6.36% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 98.20% | 0.80% | 0.60% | 0.40% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 1.10% | 2.22% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0210599887 | C -> G | LOC_Os02g18270.1 | upstream_gene_variant ; 3126.0bp to feature; MODIFIER | silent_mutation | Average:42.903; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 | N | N | N | N |
| vg0210599887 | C -> G | LOC_Os02g18280.1 | upstream_gene_variant ; 404.0bp to feature; MODIFIER | silent_mutation | Average:42.903; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 | N | N | N | N |
| vg0210599887 | C -> G | LOC_Os02g18290.1 | downstream_gene_variant ; 4290.0bp to feature; MODIFIER | silent_mutation | Average:42.903; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 | N | N | N | N |
| vg0210599887 | C -> G | LOC_Os02g18270-LOC_Os02g18280 | intergenic_region ; MODIFIER | silent_mutation | Average:42.903; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 | N | N | N | N |
| vg0210599887 | C -> DEL | N | N | silent_mutation | Average:42.903; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0210599887 | 1.62E-06 | 1.62E-06 | 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 |
| vg0210599887 | 2.86E-06 | 1.07E-08 | mr1807 | 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 |
| vg0210599887 | NA | 9.73E-07 | mr1973_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 |