| Variant ID: vg0412911460 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 12911460 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, C: 0.07, others allele: 0.00, population size: 59. )
GAAGTCCTCCGTGTCAGTTATTACCCAAAACATGTCTAAAATGAAGTCAAAGAATTTTTCAAAAATTCAAGCAAACATTAAACAAGGTGCCCGCGTATAT[T/C]
GCAGGTCCATTAAACTTCCTACAAACGTTCTCAGGCCATCACGTGGCTCCTACAAACTCTCCTAAGCCGTCACGTGGCACTCTGATAAATTAGAGAAATA
TATTTCTCTAATTTATCAGAGTGCCACGTGACGGCTTAGGAGAGTTTGTAGGAGCCACGTGATGGCCTGAGAACGTTTGTAGGAAGTTTAATGGACCTGC[A/G]
ATATACGCGGGCACCTTGTTTAATGTTTGCTTGAATTTTTGAAAAATTCTTTGACTTCATTTTAGACATGTTTTGGGTAATAACTGACACGGAGGACTTC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 44.50% | 8.10% | 2.14% | 45.22% | NA |
| All Indica | 2759 | 17.00% | 5.40% | 3.08% | 74.45% | NA |
| All Japonica | 1512 | 98.10% | 0.20% | 0.07% | 1.59% | NA |
| Aus | 269 | 9.70% | 80.30% | 3.72% | 6.32% | NA |
| Indica I | 595 | 30.60% | 1.20% | 1.34% | 66.89% | NA |
| Indica II | 465 | 25.60% | 1.30% | 4.95% | 68.17% | NA |
| Indica III | 913 | 2.20% | 11.30% | 2.96% | 83.57% | NA |
| Indica Intermediate | 786 | 19.00% | 4.30% | 3.44% | 73.28% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.00% | 1.69% | NA |
| Tropical Japonica | 504 | 99.00% | 0.20% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.80% | 0.41% | 2.90% | NA |
| VI/Aromatic | 96 | 70.80% | 9.40% | 1.04% | 18.75% | NA |
| Intermediate | 90 | 62.20% | 6.70% | 4.44% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0412911460 | T -> C | LOC_Os04g22790-LOC_Os04g22800 | intergenic_region ; MODIFIER | silent_mutation | Average:9.273; most accessible tissue: Callus, score: 48.11 | N | N | N | N |
| vg0412911460 | T -> DEL | N | N | silent_mutation | Average:9.273; most accessible tissue: Callus, score: 48.11 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0412911460 | NA | 9.87E-06 | mr1145 | 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 |
| vg0412911460 | NA | 2.04E-06 | mr1415 | 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 |
| vg0412911460 | NA | 2.04E-06 | mr1567 | 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 |
| vg0412911460 | 2.69E-06 | NA | mr1103_2 | 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 |