| Variant ID: vg0209208489 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9208489 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GACGGGCCAGGGCGGAAGGTGAGCAGCAGCGCATCCTCCGTGCTACCAATGCCGGAGGTTTCCCCCTCCTGAGGAACCACGGGCGCGGGCTCGGCACGAG[G/A]
GGTCTCCACGAAGCAGGTCCACGCCAGGGACTAACGAACAAGCTCAGGCCTGGAGGTGCTCTTGCGGGCAGTGATCTTCTGGCTGCGGCAGACGCGGCGG
CCGCCGCGTCTGCCGCAGCCAGAAGATCACTGCCCGCAAGAGCACCTCCAGGCCTGAGCTTGTTCGTTAGTCCCTGGCGTGGACCTGCTTCGTGGAGACC[C/T]
CTCGTGCCGAGCCCGCGCCCGTGGTTCCTCAGGAGGGGGAAACCTCCGGCATTGGTAGCACGGAGGATGCGCTGCTGCTCACCTTCCGCCCTGGCCCGTC
| 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 | 81.60% | 1.60% | 3.41% | 13.42% | NA |
| All Indica | 2759 | 71.30% | 2.70% | 5.76% | 20.26% | NA |
| All Japonica | 1512 | 99.10% | 0.00% | 0.00% | 0.86% | NA |
| Aus | 269 | 82.20% | 0.00% | 0.37% | 17.47% | NA |
| Indica I | 595 | 81.50% | 0.80% | 1.68% | 15.97% | NA |
| Indica II | 465 | 69.20% | 1.50% | 3.23% | 26.02% | NA |
| Indica III | 913 | 66.00% | 4.30% | 8.76% | 20.92% | NA |
| Indica Intermediate | 786 | 70.70% | 3.10% | 6.87% | 19.34% | NA |
| Temperate Japonica | 767 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 86.70% | 0.00% | 1.11% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0209208489 | G -> A | LOC_Os02g16210.1 | upstream_gene_variant ; 2200.0bp to feature; MODIFIER | silent_mutation | Average:49.695; most accessible tissue: Zhenshan97 flag leaf, score: 79.481 | N | N | N | N |
| vg0209208489 | G -> A | LOC_Os02g16190.1 | downstream_gene_variant ; 4208.0bp to feature; MODIFIER | silent_mutation | Average:49.695; most accessible tissue: Zhenshan97 flag leaf, score: 79.481 | N | N | N | N |
| vg0209208489 | G -> A | LOC_Os02g16200.1 | intron_variant ; MODIFIER | silent_mutation | Average:49.695; most accessible tissue: Zhenshan97 flag leaf, score: 79.481 | N | N | N | N |
| vg0209208489 | G -> DEL | N | N | silent_mutation | Average:49.695; most accessible tissue: Zhenshan97 flag leaf, score: 79.481 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0209208489 | NA | 2.10E-07 | mr1167_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 |
| vg0209208489 | 7.69E-06 | 1.46E-06 | mr1698_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 |
| vg0209208489 | 8.64E-07 | 4.40E-08 | mr1726_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 |