| Variant ID: vg1125308482 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 25308482 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, G: 0.05, others allele: 0.00, population size: 80. )
AGAGAAGTGAGGAGAGAGATGATGAACCATCCCTAAGTCAAGAATCAACCTCCACACAAATTTCAAGAAGAGTGTGAGAGTATTAGTGACATTGATATTT[A/G]
TGTACTAGAGGTGACATATTGTATGTGTTGCCTCTTAATTTACGAGTGAATGATATGGATAAATTTGGATATGGTAATCACATTTACCATAACACTTGCC
GGCAAGTGTTATGGTAAATGTGATTACCATATCCAAATTTATCCATATCATTCACTCGTAAATTAAGAGGCAACACATACAATATGTCACCTCTAGTACA[T/C]
AAATATCAATGTCACTAATACTCTCACACTCTTCTTGAAATTTGTGTGGAGGTTGATTCTTGACTTAGGGATGGTTCATCATCTCTCTCCTCACTTCTCT
| 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 | 42.10% | 22.20% | 0.25% | 35.46% | NA |
| All Indica | 2759 | 61.10% | 13.60% | 0.22% | 25.12% | NA |
| All Japonica | 1512 | 14.60% | 36.00% | 0.26% | 49.14% | NA |
| Aus | 269 | 17.80% | 21.90% | 0.37% | 59.85% | NA |
| Indica I | 595 | 42.90% | 6.40% | 0.34% | 50.42% | NA |
| Indica II | 465 | 27.10% | 39.60% | 0.43% | 32.90% | NA |
| Indica III | 913 | 86.70% | 4.20% | 0.00% | 9.09% | NA |
| Indica Intermediate | 786 | 65.30% | 14.50% | 0.25% | 19.97% | NA |
| Temperate Japonica | 767 | 3.00% | 55.00% | 0.13% | 41.85% | NA |
| Tropical Japonica | 504 | 31.50% | 10.90% | 0.40% | 57.14% | NA |
| Japonica Intermediate | 241 | 16.20% | 27.80% | 0.41% | 55.60% | NA |
| VI/Aromatic | 96 | 1.00% | 53.10% | 0.00% | 45.83% | NA |
| Intermediate | 90 | 35.60% | 24.40% | 1.11% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1125308482 | A -> DEL | N | N | silent_mutation | Average:63.504; most accessible tissue: Zhenshan97 root, score: 86.891 | N | N | N | N |
| vg1125308482 | A -> G | LOC_Os11g42050-LOC_Os11g42060 | intergenic_region ; MODIFIER | silent_mutation | Average:63.504; most accessible tissue: Zhenshan97 root, score: 86.891 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1125308482 | NA | 1.62E-10 | Grain_width | Ind_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1125308482 | 2.50E-06 | NA | mr1130 | 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 |
| vg1125308482 | NA | 2.79E-07 | mr1133 | 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 |