| Variant ID: vg0610398034 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 10398034 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.24, others allele: 0.00, population size: 55. )
ACAGCCATCCATTTTTATTAATGACCTAATCTCCAACTAAACTCCCTATCAATTCCATCAGCTCTACCAAACAAGATATTGGGATTAAAAATCAAATTCC[C/T]
ATCTTGATCTCGTCATAAATTCCCTCGTGTAAATTCCCAATCCCCTTCCCTCGAGTTACCAAACAAGCCGTAGTTCGATAAGAAAATTACAAGAGTTACA
TGTAACTCTTGTAATTTTCTTATCGAACTACGGCTTGTTTGGTAACTCGAGGGAAGGGGATTGGGAATTTACACGAGGGAATTTATGACGAGATCAAGAT[G/A]
GGAATTTGATTTTTAATCCCAATATCTTGTTTGGTAGAGCTGATGGAATTGATAGGGAGTTTAGTTGGAGATTAGGTCATTAATAAAAATGGATGGCTGT
| 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 | 31.10% | 3.70% | 0.83% | 64.41% | NA |
| All Indica | 2759 | 10.40% | 5.20% | 1.20% | 83.15% | NA |
| All Japonica | 1512 | 55.90% | 1.70% | 0.20% | 42.26% | NA |
| Aus | 269 | 82.20% | 0.40% | 0.74% | 16.73% | NA |
| Indica I | 595 | 10.30% | 0.50% | 0.84% | 88.40% | NA |
| Indica II | 465 | 3.70% | 5.40% | 1.29% | 89.68% | NA |
| Indica III | 913 | 11.60% | 10.30% | 0.66% | 77.44% | NA |
| Indica Intermediate | 786 | 13.20% | 2.80% | 2.04% | 81.93% | NA |
| Temperate Japonica | 767 | 55.00% | 2.00% | 0.00% | 43.02% | NA |
| Tropical Japonica | 504 | 62.70% | 0.40% | 0.20% | 36.71% | NA |
| Japonica Intermediate | 241 | 44.40% | 3.30% | 0.83% | 51.45% | NA |
| VI/Aromatic | 96 | 84.40% | 5.20% | 1.04% | 9.38% | NA |
| Intermediate | 90 | 36.70% | 0.00% | 0.00% | 63.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0610398034 | C -> T | LOC_Os06g17910.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.597; most accessible tissue: Callus, score: 40.621 | N | N | N | N |
| vg0610398034 | C -> DEL | N | N | silent_mutation | Average:14.597; most accessible tissue: Callus, score: 40.621 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0610398034 | 4.81E-06 | NA | mr1068 | 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 |
| vg0610398034 | 3.27E-09 | NA | mr1695 | 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 |
| vg0610398034 | 2.39E-09 | 5.85E-12 | mr1695 | 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 |
| vg0610398034 | 7.46E-07 | NA | mr1211_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 |
| vg0610398034 | 1.48E-08 | NA | mr1695_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 |
| vg0610398034 | 3.53E-06 | 1.43E-11 | mr1695_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 |