| Variant ID: vg1206357643 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 6357643 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 74. )
CACAATTTCACAGCTCTCGGAACCGAGCTTGGAGACCTTGCTCGCAAACCTCACCAACCTGGAGGAGCTTCGTCTGGGCATGGTGAACATGTCGAGAAAC[G/A]
GCGCACGGTGGTGCGACGCCATGGCCAGGTCCTCCCCAAAGCTGCGGGTCATTAGCATGCCGTACTGCTCACTCTCCGGTCCCATTTGCCACTCACTCTC
GAGAGTGAGTGGCAAATGGGACCGGAGAGTGAGCAGTACGGCATGCTAATGACCCGCAGCTTTGGGGAGGACCTGGCCATGGCGTCGCACCACCGTGCGC[C/T]
GTTTCTCGACATGTTCACCATGCCCAGACGAAGCTCCTCCAGGTTGGTGAGGTTTGCGAGCAAGGTCTCCAAGCTCGGTTCCGAGAGCTGTGAAATTGTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.80% | 23.90% | 4.25% | 38.04% | NA |
| All Indica | 2759 | 5.50% | 35.20% | 1.34% | 57.99% | NA |
| All Japonica | 1512 | 85.80% | 4.00% | 8.40% | 1.79% | NA |
| Aus | 269 | 36.80% | 2.60% | 9.29% | 51.30% | NA |
| Indica I | 595 | 6.70% | 85.40% | 0.67% | 7.23% | NA |
| Indica II | 465 | 3.70% | 18.70% | 1.51% | 76.13% | NA |
| Indica III | 913 | 4.10% | 10.70% | 1.20% | 84.01% | NA |
| Indica Intermediate | 786 | 7.30% | 35.40% | 1.91% | 55.47% | NA |
| Temperate Japonica | 767 | 79.10% | 6.80% | 13.04% | 1.04% | NA |
| Tropical Japonica | 504 | 93.80% | 0.80% | 2.58% | 2.78% | NA |
| Japonica Intermediate | 241 | 90.50% | 1.70% | 5.81% | 2.07% | NA |
| VI/Aromatic | 96 | 4.20% | 68.80% | 9.38% | 17.71% | NA |
| Intermediate | 90 | 50.00% | 28.90% | 3.33% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1206357643 | G -> DEL | LOC_Os12g11720.1 | N | frameshift_variant | Average:63.531; most accessible tissue: Zhenshan97 flower, score: 81.047 | N | N | N | N |
| vg1206357643 | G -> A | LOC_Os12g11720.1 | missense_variant ; p.Gly233Ser; MODERATE | nonsynonymous_codon ; G233S | Average:63.531; most accessible tissue: Zhenshan97 flower, score: 81.047 | unknown | unknown | DELETERIOUS | 0.03 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1206357643 | NA | 2.96E-18 | mr1253 | 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 |
| vg1206357643 | 2.07E-06 | NA | mr1498 | 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 |
| vg1206357643 | NA | 3.76E-24 | mr1841 | 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 |
| vg1206357643 | NA | 2.32E-23 | mr1253_2 | 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 |
| vg1206357643 | NA | 6.67E-15 | mr1578_2 | 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 |
| vg1206357643 | NA | 8.13E-06 | mr1792_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 |
| vg1206357643 | NA | 6.35E-06 | mr1927_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 |