| Variant ID: vg1202061889 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 2061889 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CATTCGCTCTATCTCTCTTACCTTTGAACCAGATCCTCGCGGCCCACTGTTCGACCGAGCGAACCATGCGGGCTCGTCTTGATGGTTTGAAGAACCGTCT[C/T]
CGAGCCAAAGATGACGAACTGGGCCGCAAGAGCCTGGAAATGGAAGGCCTCGCCCACGCCCTCAAAGAGACGAAGGCCGAGAACAAGCGGCTTCGGGCTG
CAGCCCGAAGCCGCTTGTTCTCGGCCTTCGTCTCTTTGAGGGCGTGGGCGAGGCCTTCCATTTCCAGGCTCTTGCGGCCCAGTTCGTCATCTTTGGCTCG[G/A]
AGACGGTTCTTCAAACCATCAAGACGAGCCCGCATGGTTCGCTCGGTCGAACAGTGGGCCGCGAGGATCTGGTTCAAAGGTAAGAGAGATAGAGCGAATG
| 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 | 45.20% | 30.00% | 4.82% | 19.97% | NA |
| All Indica | 2759 | 11.90% | 50.30% | 7.00% | 30.88% | NA |
| All Japonica | 1512 | 93.90% | 0.30% | 1.79% | 3.97% | NA |
| Aus | 269 | 86.60% | 4.10% | 1.49% | 7.81% | NA |
| Indica I | 595 | 12.90% | 47.20% | 11.26% | 28.57% | NA |
| Indica II | 465 | 10.50% | 69.90% | 1.94% | 17.63% | NA |
| Indica III | 913 | 8.00% | 45.60% | 8.32% | 38.12% | NA |
| Indica Intermediate | 786 | 16.30% | 46.40% | 5.22% | 32.06% | NA |
| Temperate Japonica | 767 | 94.80% | 0.40% | 1.43% | 3.39% | NA |
| Tropical Japonica | 504 | 91.10% | 0.40% | 2.98% | 5.56% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.41% | 2.49% | NA |
| VI/Aromatic | 96 | 96.90% | 2.10% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 72.20% | 12.20% | 4.44% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1202061889 | C -> DEL | LOC_Os12g04820.1 | N | frameshift_variant | Average:26.056; most accessible tissue: Zhenshan97 young leaf, score: 41.875 | N | N | N | N |
| vg1202061889 | C -> T | LOC_Os12g04820.1 | synonymous_variant ; p.Leu454Leu; LOW | synonymous_codon | Average:26.056; most accessible tissue: Zhenshan97 young leaf, score: 41.875 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1202061889 | 2.53E-06 | 4.70E-09 | mr1341_2 | 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 |
| vg1202061889 | 2.43E-06 | 2.43E-06 | mr1341_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 |