| Variant ID: vg1214403070 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 14403070 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CACTGGGGGCCAAAACCCATGTTTTGCATCAGTTCAAGTAGATATTCCCAGGAGACCGAATCAAAAGCTCTAGCAATGTCTAGCTTGAGAAAAAGTGTTG[G/C]
CTTTTTGCTGGCATTTAGGTTCCTGAGCACGTTCCGAACATACAGGAAGTTGTCTTGAATGCATCTTTTTTTGATGAAGGCGCTCTGTGCAACAGAGATC
GATCTCTGTTGCACAGAGCGCCTTCATCAAAAAAAGATGCATTCAAGACAACTTCCTGTATGTTCGGAACGTGCTCAGGAACCTAAATGCCAGCAAAAAG[C/G]
CAACACTTTTTCTCAAGCTAGACATTGCTAGAGCTTTTGATTCGGTCTCCTGGGAATATCTACTTGAACTGATGCAAAACATGGGTTTTGGCCCCCAGTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.90% | 1.00% | 6.01% | 7.05% | NA |
| All Indica | 2759 | 77.10% | 1.60% | 9.60% | 11.67% | NA |
| All Japonica | 1512 | 99.00% | 0.00% | 0.46% | 0.53% | NA |
| Aus | 269 | 95.90% | 1.10% | 2.97% | 0.00% | NA |
| Indica I | 595 | 56.00% | 1.70% | 17.98% | 24.37% | NA |
| Indica II | 465 | 78.10% | 2.80% | 11.18% | 7.96% | NA |
| Indica III | 913 | 88.90% | 1.30% | 3.07% | 6.68% | NA |
| Indica Intermediate | 786 | 78.80% | 1.30% | 9.92% | 10.05% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.65% | 0.78% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.40% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 0.00% | 4.44% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1214403070 | G -> C | LOC_Os12g25070.1 | missense_variant ; p.Pro123Ala; MODERATE | nonsynonymous_codon ; P123A | Average:13.762; most accessible tissue: Callus, score: 24.024 | unknown | unknown | TOLERATED | 0.21 |
| vg1214403070 | G -> DEL | LOC_Os12g25070.1 | N | frameshift_variant | Average:13.762; most accessible tissue: Callus, score: 24.024 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1214403070 | 9.47E-07 | NA | mr1503 | 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 |
| vg1214403070 | 4.80E-06 | NA | mr1503 | 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 |