| Variant ID: vg0326795211 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 26795211 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 109. )
AAAACCATTTTCACTGGCGGCTGGGTTAAGAGGACCGCTTGCAAAAATAGAGGTCTTTTTACAAGCGGTCCTCTTAAGTGATCGCCAGCGAAAGTTTTTC[A/G]
CTATACTAAAACACCAAGTGCGCACGGACTCTTCTTATCCACTCACTCCATCTTACCCTATTCTCCTCACCCCACCTCCATCTTATCCACTCACGCCCAC
GTGGGCGTGAGTGGATAAGATGGAGGTGGGGTGAGGAGAATAGGGTAAGATGGAGTGAGTGGATAAGAAGAGTCCGTGCGCACTTGGTGTTTTAGTATAG[T/C]
GAAAAACTTTCGCTGGCGATCACTTAAGAGGACCGCTTGTAAAAAGACCTCTATTTTTGCAAGCGGTCCTCTTAACCCAGCCGCCAGTGAAAATGGTTTT
| 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 | 54.70% | 42.40% | 0.13% | 2.77% | NA |
| All Indica | 2759 | 79.80% | 15.40% | 0.14% | 4.64% | NA |
| All Japonica | 1512 | 1.40% | 98.60% | 0.00% | 0.00% | NA |
| Aus | 269 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 83.20% | 2.20% | 0.34% | 14.29% | NA |
| Indica II | 465 | 96.60% | 3.00% | 0.00% | 0.43% | NA |
| Indica III | 913 | 65.30% | 34.20% | 0.00% | 0.55% | NA |
| Indica Intermediate | 786 | 84.40% | 10.80% | 0.25% | 4.58% | NA |
| Temperate Japonica | 767 | 0.50% | 99.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.80% | 98.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 3.30% | 96.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 58.30% | 41.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 52.20% | 42.20% | 2.22% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0326795211 | A -> DEL | N | N | silent_mutation | Average:53.441; most accessible tissue: Zhenshan97 young leaf, score: 75.397 | N | N | N | N |
| vg0326795211 | A -> G | LOC_Os03g47370.1 | downstream_gene_variant ; 3952.0bp to feature; MODIFIER | silent_mutation | Average:53.441; most accessible tissue: Zhenshan97 young leaf, score: 75.397 | N | N | N | N |
| vg0326795211 | A -> G | LOC_Os03g47390.1 | downstream_gene_variant ; 3177.0bp to feature; MODIFIER | silent_mutation | Average:53.441; most accessible tissue: Zhenshan97 young leaf, score: 75.397 | N | N | N | N |
| vg0326795211 | A -> G | LOC_Os03g47380.1 | intron_variant ; MODIFIER | silent_mutation | Average:53.441; most accessible tissue: Zhenshan97 young leaf, score: 75.397 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0326795211 | NA | 4.13E-20 | Yield | 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 |
| vg0326795211 | NA | 3.53E-19 | mr1627 | 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 |
| vg0326795211 | NA | 1.29E-07 | mr1004_2 | 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 |
| vg0326795211 | NA | 3.98E-19 | mr1383_2 | 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 |
| vg0326795211 | NA | 6.75E-22 | mr1627_2 | 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 |