| Variant ID: vg1000066190 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 66190 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 340. )
AAGATTGCCTCTGATGAAAGTGATTGTGTTGCAAGTAGATGGACAGATGAAGATAAGGGCTAGGGGCATTTGGGTAGGGGGCGGGGGAAGAGGAAGATAA[G/A]
GTTTACTTTTGGCAGAACTATGCCTCTTTAAGCTATATAGTATGCAAAAAGATACTAGTCCAAGAACATCCTAGCCGTATATAATGGCCAGTCTAAATTT
AAATTTAGACTGGCCATTATATACGGCTAGGATGTTCTTGGACTAGTATCTTTTTGCATACTATATAGCTTAAAGAGGCATAGTTCTGCCAAAAGTAAAC[C/T]
TTATCTTCCTCTTCCCCCGCCCCCTACCCAAATGCCCCTAGCCCTTATCTTCATCTGTCCATCTACTTGCAACACAATCACTTTCATCAGAGGCAATCTT
| 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 | 98.30% | 1.50% | 0.15% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 95.40% | 4.20% | 0.40% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 91.40% | 7.80% | 0.78% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 90.60% | 9.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000066190 | G -> A | LOC_Os10g01060.1 | upstream_gene_variant ; 929.0bp to feature; MODIFIER | silent_mutation | Average:68.191; most accessible tissue: Zhenshan97 young leaf, score: 81.102 | N | N | N | N |
| vg1000066190 | G -> A | LOC_Os10g01044-LOC_Os10g01060 | intergenic_region ; MODIFIER | silent_mutation | Average:68.191; most accessible tissue: Zhenshan97 young leaf, score: 81.102 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000066190 | 1.51E-06 | 7.22E-11 | Awn_length | Jap_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 |
| vg1000066190 | NA | 8.71E-06 | mr1300 | 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 |
| vg1000066190 | 3.74E-06 | 3.74E-06 | mr1470 | Jap_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 |