| Variant ID: vg1213201641 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 13201641 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CAAACCATGGCATACATCAAAGAACCAACAGCACTAGAATATGGAACTCTAGACATGTATTCTACATCCTCATCAGTATTAGCACATTGTAAAGCTGATA[A/G]
TTTAAAATGAGGTGCAATAGGAGTGCTAACAGGCTTTGCATCATGCATGTTAAAACACTGAAGAACCTTCTTAATGTAGCTTTGCTGACTAAGAAATAAC
GTTATTTCTTAGTCAGCAAAGCTACATTAAGAAGGTTCTTCAGTGTTTTAACATGCATGATGCAAAGCCTGTTAGCACTCCTATTGCACCTCATTTTAAA[T/C]
TATCAGCTTTACAATGTGCTAATACTGATGAGGATGTAGAATACATGTCTAGAGTTCCATATTCTAGTGCTGTTGGTTCTTTGATGTATGCCATGGTTTG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.80% | 0.30% | 3.07% | 11.83% | NA |
| All Indica | 2759 | 94.90% | 0.40% | 3.01% | 1.70% | NA |
| All Japonica | 1512 | 65.50% | 0.00% | 1.79% | 32.74% | NA |
| Aus | 269 | 91.80% | 0.00% | 5.95% | 2.23% | NA |
| Indica I | 595 | 96.00% | 0.50% | 2.52% | 1.01% | NA |
| Indica II | 465 | 87.30% | 0.40% | 6.67% | 5.59% | NA |
| Indica III | 913 | 99.00% | 0.10% | 0.66% | 0.22% | NA |
| Indica Intermediate | 786 | 93.80% | 0.60% | 3.94% | 1.65% | NA |
| Temperate Japonica | 767 | 83.30% | 0.00% | 1.56% | 15.12% | NA |
| Tropical Japonica | 504 | 45.20% | 0.00% | 1.59% | 53.17% | NA |
| Japonica Intermediate | 241 | 51.00% | 0.00% | 2.90% | 46.06% | NA |
| VI/Aromatic | 96 | 76.00% | 1.00% | 17.71% | 5.21% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 2.22% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1213201641 | A -> DEL | LOC_Os12g23320.1 | N | frameshift_variant | Average:10.328; most accessible tissue: Callus, score: 23.7 | N | N | N | N |
| vg1213201641 | A -> G | LOC_Os12g23320.1 | synonymous_variant ; p.Leu1086Leu; LOW | synonymous_codon | Average:10.328; most accessible tissue: Callus, score: 23.7 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1213201641 | 3.65E-06 | 1.50E-06 | mr1011 | 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 |
| vg1213201641 | 2.91E-06 | NA | mr1011 | 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 |