| Variant ID: vg0608026465 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 8026465 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 117. )
TCTCCCCTCCTTTCCTATTTATTAAGCTAACTTCTATTTTTTAAGCTAACACTCAATCTATCAAAAATTAATAATCATATTTCTAAATGATCGTAAATCT[C/T]
AAGTTAATTTTTTTCTCTTTTTTTTGAATTATTGTGCTATTTATAATTAAATACATAATTCAAGATCCATATACATAGCTCAAACTTATAATATAAATGT
ACATTTATATTATAAGTTTGAGCTATGTATATGGATCTTGAATTATGTATTTAATTATAAATAGCACAATAATTCAAAAAAAAGAGAAAAAAATTAACTT[G/A]
AGATTTACGATCATTTAGAAATATGATTATTAATTTTTGATAGATTGAGTGTTAGCTTAAAAAATAGAAGTTAGCTTAATAAATAGGAAAGGAGGGGAGA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 79.40% | 16.80% | 2.88% | 0.97% | NA |
| All Indica | 2759 | 65.00% | 28.50% | 4.86% | 1.67% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.07% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 39.50% | 47.70% | 11.43% | 1.34% | NA |
| Indica II | 465 | 92.90% | 5.80% | 0.86% | 0.43% | NA |
| Indica III | 913 | 62.70% | 31.90% | 2.85% | 2.63% | NA |
| Indica Intermediate | 786 | 70.50% | 23.40% | 4.58% | 1.53% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0608026465 | C -> T | LOC_Os06g14379-LOC_Os06g14390 | intergenic_region ; MODIFIER | silent_mutation | Average:43.809; most accessible tissue: Minghui63 panicle, score: 64.459 | N | N | N | N |
| vg0608026465 | C -> DEL | N | N | silent_mutation | Average:43.809; most accessible tissue: Minghui63 panicle, score: 64.459 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0608026465 | NA | 4.87E-11 | mr1668_2 | 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 |
| vg0608026465 | 9.71E-08 | 3.27E-11 | mr1668_2 | 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 |
| vg0608026465 | NA | 1.11E-11 | mr1709_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 |
| vg0608026465 | NA | 4.10E-09 | mr1709_2 | 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 |