| Variant ID: vg1110112955 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 10112955 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 218. )
CTTTTCTTTTGCCTCTCCCAAGCTTAGGACAATGCGAACGTAGATGATCAATTGAACCACATTCAAAGCAACGATTTGGACCACCTCTTTTCCTGTTCCT[A/G]
GCATTATTCATAGCTCGAGCAATACGGTTAGCATCCAAAGCCAAATCCTCCTCCTCGATCTGTTCGAGTTGATCATCAGATGTGGCATTAAAAACAACAA
TTGTTGTTTTTAATGCCACATCTGATGATCAACTCGAACAGATCGAGGAGGAGGATTTGGCTTTGGATGCTAACCGTATTGCTCGAGCTATGAATAATGC[T/C]
AGGAACAGGAAAAGAGGTGGTCCAAATCGTTGCTTTGAATGTGGTTCAATTGATCATCTACGTTCGCATTGTCCTAAGCTTGGGAGAGGCAAAAGAAAAG
| 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 | 62.40% | 35.90% | 0.30% | 1.33% | NA |
| All Indica | 2759 | 92.60% | 7.20% | 0.14% | 0.04% | NA |
| All Japonica | 1512 | 5.20% | 94.10% | 0.07% | 0.60% | NA |
| Aus | 269 | 90.00% | 10.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 94.30% | 5.50% | 0.17% | 0.00% | NA |
| Indica II | 465 | 98.30% | 1.30% | 0.43% | 0.00% | NA |
| Indica III | 913 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 84.10% | 15.60% | 0.13% | 0.13% | NA |
| Temperate Japonica | 767 | 2.70% | 97.10% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 10.70% | 89.10% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 1.70% | 95.00% | 0.41% | 2.90% | NA |
| VI/Aromatic | 96 | 17.70% | 20.80% | 8.33% | 53.12% | NA |
| Intermediate | 90 | 63.30% | 33.30% | 1.11% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1110112955 | A -> DEL | LOC_Os11g17990.1 | N | frameshift_variant | Average:20.448; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| vg1110112955 | A -> G | LOC_Os11g17990.1 | synonymous_variant ; p.Ala267Ala; LOW | synonymous_codon | Average:20.448; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1110112955 | 8.29E-06 | NA | mr1118 | 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 |
| vg1110112955 | NA | 5.92E-06 | mr1228 | 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 |
| vg1110112955 | NA | 2.25E-13 | mr1281 | 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 |
| vg1110112955 | NA | 3.78E-09 | mr1595 | 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 |