| Variant ID: vg1216690134 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16690134 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 93. )
TATTATTTGTATGATGCACATATTTTTTAAATTAGGAAAAACCATAATCAATTAATGGCTTGGATTTAGTTAGAGCTCTTAATTGCAGTTCCTTAGTTAC[T/C]
AGAGGCTCAGAATACCTTAAAATTCCGCAGCTAGATTAACATATGCAGTGGTTAGTGGCCATATATAGTTTTTTTTCCTAATAAAACTAGAGAAATCATG
CATGATTTCTCTAGTTTTATTAGGAAAAAAAACTATATATGGCCACTAACCACTGCATATGTTAATCTAGCTGCGGAATTTTAAGGTATTCTGAGCCTCT[A/G]
GTAACTAAGGAACTGCAATTAAGAGCTCTAACTAAATCCAAGCCATTAATTGATTATGGTTTTTCCTAATTTAAAAAATATGTGCATCATACAAATAATA
| 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 | 60.20% | 9.00% | 0.85% | 29.96% | NA |
| All Indica | 2759 | 64.40% | 14.80% | 0.29% | 20.55% | NA |
| All Japonica | 1512 | 56.00% | 0.70% | 1.85% | 41.47% | NA |
| Aus | 269 | 55.00% | 0.70% | 1.49% | 42.75% | NA |
| Indica I | 595 | 87.90% | 2.50% | 0.34% | 9.24% | NA |
| Indica II | 465 | 38.70% | 38.90% | 0.22% | 22.15% | NA |
| Indica III | 913 | 65.30% | 9.30% | 0.11% | 25.30% | NA |
| Indica Intermediate | 786 | 60.70% | 16.20% | 0.51% | 22.65% | NA |
| Temperate Japonica | 767 | 86.60% | 0.50% | 0.39% | 12.52% | NA |
| Tropical Japonica | 504 | 9.70% | 1.00% | 4.37% | 84.92% | NA |
| Japonica Intermediate | 241 | 55.60% | 0.40% | 1.24% | 42.74% | NA |
| VI/Aromatic | 96 | 14.60% | 1.00% | 0.00% | 84.38% | NA |
| Intermediate | 90 | 66.70% | 4.40% | 0.00% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216690134 | T -> C | LOC_Os12g28250.1 | intron_variant ; MODIFIER | silent_mutation | Average:21.16; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg1216690134 | T -> DEL | N | N | silent_mutation | Average:21.16; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1216690134 | 7.73E-06 | 3.64E-09 | 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 |
| vg1216690134 | NA | 2.44E-11 | mr1425 | 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 |
| vg1216690134 | NA | 1.27E-07 | mr1458 | 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 |
| vg1216690134 | NA | 8.28E-06 | mr1912 | 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 |
| vg1216690134 | NA | 9.27E-07 | mr1024_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 |
| vg1216690134 | NA | 2.29E-07 | mr1458_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 |