| Variant ID: vg0621438164 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 21438164 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.01, others allele: 0.00, population size: 213. )
GAAGATAATCTGAAATGTGCAGTTAAAGGAGTACTCACTGGTTTTGCATCATACATATTGAAACGATGAAGAATTTTTTCAATATAACCTTTCTGACTAA[G/T]
ATATAACTAGCCAGAATGTCTTTCTCTAGTAATTTCCATACCGAGAATTTTCTTCGCTGCACCCAAATCCTTCATCTCAAATTCACTACTCAATTGTGCC
GGCACAATTGAGTAGTGAATTTGAGATGAAGGATTTGGGTGCAGCGAAGAAAATTCTCGGTATGGAAATTACTAGAGAAAGACATTCTGGCTAGTTATAT[C/A]
TTAGTCAGAAAGGTTATATTGAAAAAATTCTTCATCGTTTCAATATGTATGATGCAAAACCAGTGAGTACTCCTTTAACTGCACATTTCAGATTATCTTC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.20% | 20.30% | 1.46% | 0.00% | NA |
| All Indica | 2759 | 65.50% | 32.00% | 2.46% | 0.00% | NA |
| All Japonica | 1512 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.10% | 4.20% | 0.67% | 0.00% | NA |
| Indica II | 465 | 81.30% | 18.50% | 0.22% | 0.00% | NA |
| Indica III | 913 | 37.80% | 56.80% | 5.37% | 0.00% | NA |
| Indica Intermediate | 786 | 66.00% | 32.20% | 1.78% | 0.00% | NA |
| Temperate Japonica | 767 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 89.50% | 10.50% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 13.30% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0621438164 | G -> T | LOC_Os06g36490.1 | upstream_gene_variant ; 2462.0bp to feature; MODIFIER | silent_mutation | Average:26.499; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0621438164 | G -> T | LOC_Os06g36500.1 | intron_variant ; MODIFIER | silent_mutation | Average:26.499; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0621438164 | 1.26E-07 | 9.67E-08 | mr1697 | 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 |
| vg0621438164 | 1.44E-06 | 3.75E-06 | mr1697 | 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 |