| Variant ID: vg0620619367 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20619367 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, A: 0.11, others allele: 0.00, population size: 103. )
CCGAACCTCACGTTTCGTGCATCTTCGCCGAAGTCTTTAAATGTTCTGTTGATATTTCGCCACTGCGACCCGTCAGCGGGGTGTCTCAGCATCCCATCCT[A/G]
TTTACGTTCTTCTGCGTGCCACCGCATCATTCTAGCATGTGATTTGTTCCTGAAAAACCGCTTCAGCCTTGGTATTATAGGGAAATACCACATCACTTTA
TAAAGTGATGTGGTATTTCCCTATAATACCAAGGCTGAAGCGGTTTTTCAGGAACAAATCACATGCTAGAATGATGCGGTGGCACGCAGAAGAACGTAAA[T/C]
AGGATGGGATGCTGAGACACCCCGCTGACGGGTCGCAGTGGCGAAATATCAACAGAACATTTAAAGACTTCGGCGAAGATGCACGAAACGTGAGGTTCGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.10% | 3.90% | 36.03% | 30.94% | NA |
| All Indica | 2759 | 24.10% | 0.30% | 27.65% | 47.95% | NA |
| All Japonica | 1512 | 41.10% | 10.10% | 42.26% | 6.61% | NA |
| Aus | 269 | 18.60% | 0.00% | 75.84% | 5.58% | NA |
| Indica I | 595 | 6.60% | 0.00% | 16.13% | 77.31% | NA |
| Indica II | 465 | 33.50% | 0.00% | 26.88% | 39.57% | NA |
| Indica III | 913 | 31.00% | 0.30% | 35.82% | 32.86% | NA |
| Indica Intermediate | 786 | 23.90% | 0.50% | 27.35% | 48.22% | NA |
| Temperate Japonica | 767 | 72.80% | 2.90% | 15.51% | 8.87% | NA |
| Tropical Japonica | 504 | 5.00% | 12.90% | 78.77% | 3.37% | NA |
| Japonica Intermediate | 241 | 15.80% | 27.00% | 51.04% | 6.22% | NA |
| VI/Aromatic | 96 | 10.40% | 25.00% | 60.42% | 4.17% | NA |
| Intermediate | 90 | 31.10% | 3.30% | 43.33% | 22.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620619367 | A -> G | LOC_Os06g35360.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:9.268; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0620619367 | A -> G | LOC_Os06g35350.1 | upstream_gene_variant ; 4408.0bp to feature; MODIFIER | silent_mutation | Average:9.268; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0620619367 | A -> G | LOC_Os06g35370.1 | downstream_gene_variant ; 1808.0bp to feature; MODIFIER | silent_mutation | Average:9.268; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0620619367 | A -> DEL | N | N | silent_mutation | Average:9.268; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0620619367 | 5.96E-06 | 1.06E-11 | mr1660_2 | 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 |
| vg0620619367 | NA | 6.89E-06 | mr1660_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 |
| vg0620619367 | 1.43E-06 | NA | mr1699_2 | 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 |
| vg0620619367 | NA | 1.42E-06 | mr1895_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 |