| Variant ID: vg0202353698 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 2353698 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, G: 0.03, others allele: 0.00, population size: 209. )
CCACAAGTCTCCCACCTCAAAAGCTAAACAGTCTCAGCATCTGCCTCAGCAACAACAGTTCGCTGTTGAGAAAGATCAGTGTCTCCACTGCAAGAAGACA[T/G]
GACATTACAAGAAAGACTGTCCTGACTTCCTGAAAATGATCATGGCAAGGAAATGTGAAAACATTATTACATTTGTAAATGAATCTCACTATGTTGGTTA
TAACCAACATAGTGAGATTCATTTACAAATGTAATAATGTTTTCACATTTCCTTGCCATGATCATTTTCAGGAAGTCAGGACAGTCTTTCTTGTAATGTC[A/C]
TGTCTTCTTGCAGTGGAGACACTGATCTTTCTCAACAGCGAACTGTTGTTGCTGAGGCAGATGCTGAGACTGTTTAGCTTTTGAGGTGGGAGACTTGTGG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 60.40% | 16.70% | 5.16% | 17.73% | NA |
| All Indica | 2759 | 62.30% | 2.50% | 7.97% | 27.22% | NA |
| All Japonica | 1512 | 55.40% | 44.00% | 0.07% | 0.46% | NA |
| Aus | 269 | 86.20% | 11.50% | 1.49% | 0.74% | NA |
| Indica I | 595 | 67.70% | 6.40% | 3.19% | 22.69% | NA |
| Indica II | 465 | 76.30% | 0.40% | 3.23% | 20.00% | NA |
| Indica III | 913 | 44.60% | 1.20% | 14.46% | 39.76% | NA |
| Indica Intermediate | 786 | 70.50% | 2.30% | 6.87% | 20.36% | NA |
| Temperate Japonica | 767 | 89.00% | 11.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 11.50% | 88.10% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 40.20% | 57.30% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 10.40% | 1.00% | 15.62% | 72.92% | NA |
| Intermediate | 90 | 62.20% | 24.40% | 4.44% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0202353698 | T -> G | LOC_Os02g04980.1 | intron_variant ; MODIFIER | silent_mutation | Average:31.63; most accessible tissue: Zhenshan97 flag leaf, score: 52.255 | N | N | N | N |
| vg0202353698 | T -> DEL | N | N | silent_mutation | Average:31.63; most accessible tissue: Zhenshan97 flag leaf, score: 52.255 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0202353698 | 1.88E-06 | NA | Grain_length | All | YES | 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 |
| vg0202353698 | 1.16E-07 | 2.75E-12 | Grain_weight | 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 |
| vg0202353698 | NA | 5.34E-06 | mr1959_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 |