| Variant ID: vg1209423376 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9423376 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 89. )
CCGAGCAACCGGGGAAACGCCTTTCTTCCTCGTCTACGGAGCGGAGGCGGTTCTCCCATCCGAGCTCACCCTGAGGTCCCCTCGGGCCACCATGTACTGC[A/G]
AGGTGATCAAGATCAGCTTCGCAGAGATGACCTCGACTACTTGGAAGAACGAAGGCGGCGTGCGGCCCTTCGAGCCGCGCAGTACCAGCAGAGCCTGCGG
CCGCAGGCTCTGCTGGTACTGCGCGGCTCGAAGGGCCGCACGCCGCCTTCGTTCTTCCAAGTAGTCGAGGTCATCTCTGCGAAGCTGATCTTGATCACCT[T/C]
GCAGTACATGGTGGCCCGAGGGGACCTCAGGGTGAGCTCGGATGGGAGAACCGCCTCCGCTCCGTAGACGAGGAAGAAAGGCGTTTCCCCGGTTGCTCGG
| 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 | 54.00% | 13.30% | 23.38% | 9.31% | NA |
| All Indica | 2759 | 34.40% | 20.20% | 31.68% | 13.77% | NA |
| All Japonica | 1512 | 86.60% | 2.60% | 10.45% | 0.40% | NA |
| Aus | 269 | 59.90% | 5.90% | 15.24% | 18.96% | NA |
| Indica I | 595 | 33.10% | 11.40% | 48.07% | 7.39% | NA |
| Indica II | 465 | 33.30% | 15.70% | 22.37% | 28.60% | NA |
| Indica III | 913 | 37.00% | 29.10% | 24.32% | 9.53% | NA |
| Indica Intermediate | 786 | 32.80% | 19.10% | 33.33% | 14.76% | NA |
| Temperate Japonica | 767 | 91.80% | 2.30% | 5.48% | 0.39% | NA |
| Tropical Japonica | 504 | 81.30% | 4.00% | 14.48% | 0.20% | NA |
| Japonica Intermediate | 241 | 80.90% | 0.40% | 17.84% | 0.83% | NA |
| VI/Aromatic | 96 | 82.30% | 8.30% | 8.33% | 1.04% | NA |
| Intermediate | 90 | 62.20% | 8.90% | 26.67% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209423376 | A -> DEL | LOC_Os12g16450.1 | N | frameshift_variant | Average:70.943; most accessible tissue: Zhenshan97 flag leaf, score: 86.987 | N | N | N | N |
| vg1209423376 | A -> G | LOC_Os12g16450.1 | missense_variant ; p.Lys1262Glu; MODERATE | nonsynonymous_codon ; K1262E | Average:70.943; most accessible tissue: Zhenshan97 flag leaf, score: 86.987 | unknown | unknown | TOLERATED | 1.00 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1209423376 | NA | 6.80E-07 | mr1177 | Jap_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 |
| vg1209423376 | NA | 8.09E-06 | mr1322 | Jap_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 |
| vg1209423376 | 5.47E-07 | 1.31E-08 | mr1338 | Jap_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 |
| vg1209423376 | 5.73E-06 | 3.34E-06 | mr1350 | 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 |
| vg1209423376 | NA | 2.03E-08 | mr1558_2 | Jap_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 |