| Variant ID: vg1218458718 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18458718 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.22, others allele: 0.00, population size: 41. )
GAATGAGCTCCTCGGCAGCGACAACGATGAGCTTGATGCCTACTGGCCTCTCCTCAATTCGGCACTGCCGGCTATCAATTTGATGGGGCGGCGCCTCGAA[C/T]
AGAAGGCTAAGGAGGGAGCAGAAGGAGGTCCAGGAGAGGCACATTCGATGGCCAGAGGAGGAGGTGGAGCCGGTGGTCTCGATCAGAGTGGCTCCGTCGA
TCGACGGAGCCACTCTGATCGAGACCACCGGCTCCACCTCCTCCTCTGGCCATCGAATGTGCCTCTCCTGGACCTCCTTCTGCTCCCTCCTTAGCCTTCT[G/A]
TTCGAGGCGCCGCCCCATCAAATTGATAGCCGGCAGTGCCGAATTGAGGAGAGGCCAGTAGGCATCAAGCTCATCGTTGTCGCTGCCGAGGAGCTCATTC
| 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 | 80.00% | 10.10% | 1.06% | 8.84% | NA |
| All Indica | 2759 | 67.60% | 16.50% | 1.63% | 14.35% | NA |
| All Japonica | 1512 | 99.20% | 0.40% | 0.00% | 0.40% | NA |
| Aus | 269 | 95.50% | 1.90% | 0.00% | 2.60% | NA |
| Indica I | 595 | 46.10% | 34.50% | 2.02% | 17.48% | NA |
| Indica II | 465 | 82.40% | 8.40% | 1.08% | 8.17% | NA |
| Indica III | 913 | 72.40% | 8.20% | 1.97% | 17.42% | NA |
| Indica Intermediate | 786 | 69.50% | 17.20% | 1.27% | 12.09% | NA |
| Temperate Japonica | 767 | 99.20% | 0.40% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 99.20% | 0.40% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 87.50% | 6.20% | 0.00% | 6.25% | NA |
| Intermediate | 90 | 84.40% | 6.70% | 5.56% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218458718 | C -> DEL | LOC_Os12g30730.1 | N | frameshift_variant | Average:36.904; most accessible tissue: Callus, score: 58.641 | N | N | N | N |
| vg1218458718 | C -> T | LOC_Os12g30730.1 | synonymous_variant ; p.Leu59Leu; LOW | synonymous_codon | Average:36.904; most accessible tissue: Callus, score: 58.641 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1218458718 | 1.71E-06 | 1.71E-06 | mr1193 | 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 |
| vg1218458718 | NA | 1.27E-06 | mr1321 | 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 |