| Variant ID: vg0320942236 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 20942236 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 120. )
TTACATATGTAATTTTAGTTATATAAGACTGTAATTTTATATTTTAAAGAAAATAATAAGTACATATTTACTTACACATTATTTTTATCAAAATTACAGT[G/A]
CACTTACATGTAAATCAACTAAATTTACAAATGTAATTTTAGTTATATAGGACTGTAATTTTATATTTTAAAGAAAATAATAAGTACATATTTACTAACA
TGTTAGTAAATATGTACTTATTATTTTCTTTAAAATATAAAATTACAGTCCTATATAACTAAAATTACATTTGTAAATTTAGTTGATTTACATGTAAGTG[C/T]
ACTGTAATTTTGATAAAAATAATGTGTAAGTAAATATGTACTTATTATTTTCTTTAAAATATAAAATTACAGTCTTATATAACTAAAATTACATATGTAA
| 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 | 41.70% | 7.80% | 18.54% | 31.95% | NA |
| All Indica | 2759 | 28.30% | 12.60% | 12.79% | 46.21% | NA |
| All Japonica | 1512 | 57.00% | 0.10% | 32.47% | 10.38% | NA |
| Aus | 269 | 79.20% | 4.80% | 1.86% | 14.13% | NA |
| Indica I | 595 | 44.20% | 4.70% | 9.24% | 41.85% | NA |
| Indica II | 465 | 21.70% | 9.00% | 15.91% | 53.33% | NA |
| Indica III | 913 | 25.20% | 20.20% | 11.28% | 43.37% | NA |
| Indica Intermediate | 786 | 23.90% | 12.10% | 15.39% | 48.60% | NA |
| Temperate Japonica | 767 | 44.70% | 0.10% | 42.63% | 12.52% | NA |
| Tropical Japonica | 504 | 73.60% | 0.20% | 19.05% | 7.14% | NA |
| Japonica Intermediate | 241 | 61.40% | 0.00% | 28.22% | 10.37% | NA |
| VI/Aromatic | 96 | 81.20% | 0.00% | 9.38% | 9.38% | NA |
| Intermediate | 90 | 40.00% | 5.60% | 20.00% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0320942236 | G -> A | LOC_Os03g37760.1 | downstream_gene_variant ; 4669.0bp to feature; MODIFIER | silent_mutation | Average:9.441; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0320942236 | G -> A | LOC_Os03g37770.1 | downstream_gene_variant ; 1780.0bp to feature; MODIFIER | silent_mutation | Average:9.441; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0320942236 | G -> A | LOC_Os03g37780.1 | downstream_gene_variant ; 2792.0bp to feature; MODIFIER | silent_mutation | Average:9.441; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0320942236 | G -> A | LOC_Os03g37770-LOC_Os03g37780 | intergenic_region ; MODIFIER | silent_mutation | Average:9.441; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0320942236 | G -> DEL | N | N | silent_mutation | Average:9.441; 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 |
|---|---|---|---|---|---|---|
| vg0320942236 | 7.89E-06 | 7.88E-06 | mr1494 | 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 |
| vg0320942236 | 3.56E-06 | 3.56E-06 | mr1494 | 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 |
| vg0320942236 | NA | 1.02E-07 | mr1785 | 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 |