| Variant ID: vg1208951133 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 8951133 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.69, C: 0.29, others allele: 0.00, population size: 72. )
GTTGATCCACGTTCTGTATCAGTACTGGTCGAAGTTGTAATCTCTGGAGGTCCATCTCGAGCAGCATCAACAGTACCCGAACCCGACGAGCCTGGTCAGT[T/C]
TGACCGCACCTCCTGTGCCGGTCTGACCGGAGGTGTGCCGGCGGTCTGACCAGCCTGGCGTCCGGTTTGACCAGCCGAGCCGACCTTGTCATCGTTGTCG
CGACAACGATGACAAGGTCGGCTCGGCTGGTCAAACCGGACGCCAGGCTGGTCAGACCGCCGGCACACCTCCGGTCAGACCGGCACAGGAGGTGCGGTCA[A/G]
ACTGACCAGGCTCGTCGGGTTCGGGTACTGTTGATGCTGCTCGAGATGGACCTCCAGAGATTACAACTTCGACCAGTACTGATACAGAACGTGGATCAAC
| 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 | 53.20% | 35.60% | 8.72% | 2.52% | NA |
| All Indica | 2759 | 76.60% | 5.80% | 13.77% | 3.81% | NA |
| All Japonica | 1512 | 4.50% | 94.40% | 0.53% | 0.60% | NA |
| Aus | 269 | 84.40% | 7.40% | 7.06% | 1.12% | NA |
| Indica I | 595 | 63.70% | 9.40% | 22.52% | 4.37% | NA |
| Indica II | 465 | 72.70% | 6.20% | 13.33% | 7.74% | NA |
| Indica III | 913 | 85.10% | 3.20% | 9.31% | 2.41% | NA |
| Indica Intermediate | 786 | 78.80% | 6.00% | 12.60% | 2.67% | NA |
| Temperate Japonica | 767 | 6.00% | 92.70% | 0.78% | 0.52% | NA |
| Tropical Japonica | 504 | 3.60% | 95.60% | 0.20% | 0.60% | NA |
| Japonica Intermediate | 241 | 1.70% | 97.10% | 0.41% | 0.83% | NA |
| VI/Aromatic | 96 | 72.90% | 24.00% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 40.00% | 55.60% | 2.22% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1208951133 | T -> C | LOC_Os12g15670.1 | intron_variant ; MODIFIER | silent_mutation | Average:32.447; most accessible tissue: Minghui63 young leaf, score: 77.243 | N | N | N | N |
| vg1208951133 | T -> DEL | N | N | silent_mutation | Average:32.447; most accessible tissue: Minghui63 young leaf, score: 77.243 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1208951133 | NA | 2.09E-06 | mr1088 | 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 |
| vg1208951133 | 2.29E-06 | 5.37E-06 | mr1163 | 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 |
| vg1208951133 | NA | 3.82E-08 | mr1425 | 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 |
| vg1208951133 | NA | 9.58E-07 | mr1425 | 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 |
| vg1208951133 | NA | 1.23E-09 | mr1576_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 |
| vg1208951133 | NA | 6.70E-07 | mr1882_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 |