| Variant ID: vg0819590125 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 19590125 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACACATCATAAGCATGGGTTAATCTAAAACCGACATAGACACAAATGAGCTTTTTCCCGTCATTCTAAGCCTTAGAGGGGTAAAAATTTAAAACTGGCAC[C/A]
TATAACACCTTGTAGGTACTGGTTTATTAAAAGAACCGGTTCATATAATTCCCATGCCTGTTTTTTTAATGAGTAAATTACACTATGGTCCTTAAACTTG
CAAGTTTAAGGACCATAGTGTAATTTACTCATTAAAAAAACAGGCATGGGAATTATATGAACCGGTTCTTTTAATAAACCAGTACCTACAAGGTGTTATA[G/T]
GTGCCAGTTTTAAATTTTTACCCCTCTAAGGCTTAGAATGACGGGAAAAAGCTCATTTGTGTCTATGTCGGTTTTAGATTAACCCATGCTTATGATGTGT
| 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 | 54.40% | 5.60% | 26.28% | 13.67% | NA |
| All Indica | 2759 | 30.20% | 9.40% | 39.94% | 20.44% | NA |
| All Japonica | 1512 | 93.50% | 0.00% | 4.30% | 2.25% | NA |
| Aus | 269 | 74.00% | 0.00% | 14.87% | 11.15% | NA |
| Indica I | 595 | 32.80% | 2.40% | 50.25% | 14.62% | NA |
| Indica II | 465 | 20.60% | 3.90% | 45.38% | 30.11% | NA |
| Indica III | 913 | 35.30% | 14.70% | 31.11% | 18.95% | NA |
| Indica Intermediate | 786 | 28.00% | 12.00% | 39.19% | 20.87% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.26% | 0.26% | NA |
| Tropical Japonica | 504 | 84.30% | 0.00% | 10.12% | 5.56% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.00% | 4.98% | 1.66% | NA |
| VI/Aromatic | 96 | 71.90% | 1.00% | 14.58% | 12.50% | NA |
| Intermediate | 90 | 65.60% | 4.40% | 23.33% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0819590125 | C -> A | LOC_Os08g31630-LOC_Os08g31649 | intergenic_region ; MODIFIER | silent_mutation | Average:51.709; most accessible tissue: Minghui63 root, score: 63.193 | N | N | N | N |
| vg0819590125 | C -> DEL | N | N | silent_mutation | Average:51.709; most accessible tissue: Minghui63 root, score: 63.193 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0819590125 | 3.56E-06 | 8.04E-09 | mr1672_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 |
| vg0819590125 | NA | 4.50E-06 | mr1996_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 |