| Variant ID: vg0316850166 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 16850166 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGCATTAACATCTCTAATTTTTGAAATCTCATTCATTAAAACCTCACAATTTTCGCAATCATCATCATTAGGAATAAGAGATTTTAATCTAGCAATTTCA[G/T]
ATTTAAGAGATTCAATGATAAATTCCTGTTTTCTATATACATCTTCTCACACTTCTTATTCTTTTCACTCAAAATATTAATAGCTTCCTCAAAAGCACTT
AAGTGCTTTTGAGGAAGCTATTAATATTTTGAGTGAAAAGAATAAGAAGTGTGAGAAGATGTATATAGAAAACAGGAATTTATCATTGAATCTCTTAAAT[C/A]
TGAAATTGCTAGATTAAAATCTCTTATTCCTAATGATGATGATTGCGAAAATTGTGAGGTTTTAATGAATGAGATTTCAAAAATTAGAGATGTTAATGCT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 62.80% | 35.20% | 1.95% | 0.04% | NA |
| All Indica | 2759 | 42.00% | 56.70% | 1.27% | 0.00% | NA |
| All Japonica | 1512 | 96.00% | 3.80% | 0.07% | 0.07% | NA |
| Aus | 269 | 93.30% | 5.90% | 0.74% | 0.00% | NA |
| Indica I | 595 | 10.60% | 86.10% | 3.36% | 0.00% | NA |
| Indica II | 465 | 83.90% | 15.70% | 0.43% | 0.00% | NA |
| Indica III | 913 | 37.10% | 62.20% | 0.66% | 0.00% | NA |
| Indica Intermediate | 786 | 46.80% | 52.30% | 0.89% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 88.70% | 11.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 42.70% | 5.20% | 51.04% | 1.04% | NA |
| Intermediate | 90 | 73.30% | 21.10% | 5.56% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0316850166 | G -> T | LOC_Os03g29560.1 | intron_variant ; MODIFIER | silent_mutation | Average:15.367; most accessible tissue: Minghui63 flower, score: 26.22 | N | N | N | N |
| vg0316850166 | G -> DEL | N | N | silent_mutation | Average:15.367; most accessible tissue: Minghui63 flower, score: 26.22 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0316850166 | NA | 8.79E-19 | Grain_length | 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 |
| vg0316850166 | 6.72E-06 | 5.04E-08 | mr1668_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 |