| Variant ID: vg0816750102 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 16750102 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, A: 0.02, others allele: 0.00, population size: 107. )
GGCGGCGGCGTACTCACCTCCCAGATCCGGACGCGACCCTTCCCTCCCCTCACCCCCCGGATCCAGCAGCTCCCCTCTCCACCCTCTCCCTTCCAAAACC[C/A]
TAACCGAGAGGGGAGGGCGGCGGTGGGTTGGGCTGGGGCGCCGAATTTTTATACGCTTAAAAATATTTTCGCAAGCAGGTGGATTTAGCCGCCTGCAATA
TATTGCAGGCGGCTAAATCCACCTGCTTGCGAAAATATTTTTAAGCGTATAAAAATTCGGCGCCCCAGCCCAACCCACCGCCGCCCTCCCCTCTCGGTTA[G/T]
GGTTTTGGAAGGGAGAGGGTGGAGAGGGGAGCTGCTGGATCCGGGGGGTGAGGGGAGGGAAGGGTCGCGTCCGGATCTGGGAGGTGAGTACGCCGCCGCC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 42.70% | 28.70% | 3.39% | 25.22% | NA |
| All Indica | 2759 | 16.80% | 35.70% | 5.65% | 41.83% | NA |
| All Japonica | 1512 | 88.20% | 10.40% | 0.07% | 1.32% | NA |
| Aus | 269 | 28.30% | 69.90% | 0.74% | 1.12% | NA |
| Indica I | 595 | 13.90% | 68.60% | 2.52% | 14.96% | NA |
| Indica II | 465 | 28.40% | 11.20% | 9.03% | 51.40% | NA |
| Indica III | 913 | 9.40% | 26.40% | 5.37% | 58.82% | NA |
| Indica Intermediate | 786 | 20.70% | 36.10% | 6.36% | 36.77% | NA |
| Temperate Japonica | 767 | 98.60% | 0.30% | 0.13% | 1.04% | NA |
| Tropical Japonica | 504 | 69.80% | 28.20% | 0.00% | 1.98% | NA |
| Japonica Intermediate | 241 | 93.80% | 5.40% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 94.80% | 4.20% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 61.10% | 22.20% | 1.11% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0816750102 | C -> A | LOC_Os08g27430.1 | downstream_gene_variant ; 3760.0bp to feature; MODIFIER | silent_mutation | Average:34.962; most accessible tissue: Zhenshan97 flag leaf, score: 80.156 | N | N | N | N |
| vg0816750102 | C -> A | LOC_Os08g27440.1 | intron_variant ; MODIFIER | silent_mutation | Average:34.962; most accessible tissue: Zhenshan97 flag leaf, score: 80.156 | N | N | N | N |
| vg0816750102 | C -> DEL | N | N | silent_mutation | Average:34.962; most accessible tissue: Zhenshan97 flag leaf, score: 80.156 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0816750102 | NA | 1.21E-06 | mr1071 | 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 |
| vg0816750102 | NA | 4.27E-06 | mr1080 | 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 |
| vg0816750102 | NA | 3.09E-06 | mr1203 | 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 |
| vg0816750102 | 8.28E-06 | 7.81E-08 | mr1395 | 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 |
| vg0816750102 | NA | 6.34E-06 | mr1618 | 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 |
| vg0816750102 | NA | 1.67E-08 | mr1613_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 |