| Variant ID: vg0431619094 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 31619094 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 62. )
CACAGTTCGTGCCATGGCCAGATTTACATAGCAGATGGTGCATGCGACATTTTGGGGCTAATTTTTATAGACAATTTAGGAGTAAGAGATTGATGGACCT[G/A]
TTCAAGAAGTTATGCAAGCAGAATTAACAAAGAAAGTTTGATGCCATATGGGATCAACTGGATCGTTTGACCACTACACACATGGAAGAGGTTAGGAAAA
TTTTCCTAACCTCTTCCATGTGTGTAGTGGTCAAACGATCCAGTTGATCCCATATGGCATCAAACTTTCTTTGTTAATTCTGCTTGCATAACTTCTTGAA[C/T]
AGGTCCATCAATCTCTTACTCCTAAATTGTCTATAAAAATTAGCCCCAAAATGTCGCATGCACCATCTGCTATGTAAATCTGGCCATGGCACGAACTGTG
| 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 | 22.20% | 5.50% | 5.84% | 66.38% | NA |
| All Indica | 2759 | 8.80% | 7.40% | 7.76% | 76.04% | NA |
| All Japonica | 1512 | 49.60% | 1.70% | 1.85% | 46.89% | NA |
| Aus | 269 | 9.70% | 8.90% | 8.55% | 72.86% | NA |
| Indica I | 595 | 15.60% | 10.80% | 22.02% | 51.60% | NA |
| Indica II | 465 | 9.70% | 3.40% | 1.08% | 85.81% | NA |
| Indica III | 913 | 3.10% | 9.00% | 3.61% | 84.34% | NA |
| Indica Intermediate | 786 | 9.90% | 5.20% | 5.73% | 79.13% | NA |
| Temperate Japonica | 767 | 82.00% | 0.70% | 0.52% | 16.82% | NA |
| Tropical Japonica | 504 | 8.30% | 2.60% | 3.37% | 85.71% | NA |
| Japonica Intermediate | 241 | 32.80% | 2.90% | 2.90% | 61.41% | NA |
| VI/Aromatic | 96 | 9.40% | 4.20% | 2.08% | 84.38% | NA |
| Intermediate | 90 | 24.40% | 6.70% | 10.00% | 58.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0431619094 | G -> DEL | N | N | silent_mutation | Average:9.947; most accessible tissue: Zhenshan97 flower, score: 17.42 | N | N | N | N |
| vg0431619094 | G -> A | LOC_Os04g53080-LOC_Os04g53110 | intergenic_region ; MODIFIER | silent_mutation | Average:9.947; most accessible tissue: Zhenshan97 flower, score: 17.42 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0431619094 | NA | 6.01E-06 | mr1102_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 |
| vg0431619094 | NA | 8.24E-06 | mr1236_2 | Jap_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 |
| vg0431619094 | NA | 6.51E-09 | mr1800_2 | Jap_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 |