| Variant ID: vg1218136630 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18136630 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, T: 0.16, others allele: 0.00, population size: 159. )
AGTTGAAAGAAAAGGGGTACATACGTCCGAGTACTTCCCCATGGGGTGCTCCTGTGATTTTTGTAGAGAAGAAAGACAAGACGAAGAGGATGTGCGTCGA[T/C]
TACAGAGCTCTCAATGAAGTCACCATCAAAAACAAGTACCCTCTTCCCCGGATCGATGATCTATTCGATCAGCTTAAAGGTGCCACTGTATTCTCCAAGA
TCTTGGAGAATACAGTGGCACCTTTAAGCTGATCGAATAGATCATCGATCCGGGGAAGAGGGTACTTGTTTTTGATGGTGACTTCATTGAGAGCTCTGTA[A/G]
TCGACGCACATCCTCTTCGTCTTGTCTTTCTTCTCTACAAAAATCACAGGAGCACCCCATGGGGAAGTACTCGGACGTATGTACCCCTTTTCTTTCAACT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.50% | 0.10% | 11.60% | 37.81% | NA |
| All Indica | 2759 | 38.60% | 0.10% | 17.58% | 43.75% | NA |
| All Japonica | 1512 | 68.10% | 0.00% | 2.45% | 29.50% | NA |
| Aus | 269 | 57.20% | 0.40% | 7.06% | 35.32% | NA |
| Indica I | 595 | 31.80% | 0.00% | 4.03% | 64.20% | NA |
| Indica II | 465 | 38.90% | 0.20% | 21.08% | 39.78% | NA |
| Indica III | 913 | 41.60% | 0.10% | 28.37% | 29.90% | NA |
| Indica Intermediate | 786 | 39.90% | 0.10% | 13.23% | 46.69% | NA |
| Temperate Japonica | 767 | 76.70% | 0.00% | 0.39% | 22.95% | NA |
| Tropical Japonica | 504 | 50.60% | 0.00% | 5.16% | 44.25% | NA |
| Japonica Intermediate | 241 | 77.20% | 0.00% | 3.32% | 19.50% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 2.08% | 13.54% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 5.56% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218136630 | T -> C | LOC_Os12g30214.1 | synonymous_variant ; p.Asp944Asp; LOW | synonymous_codon | Average:9.53; most accessible tissue: Callus, score: 20.931 | N | N | N | N |
| vg1218136630 | T -> DEL | LOC_Os12g30214.1 | N | frameshift_variant | Average:9.53; most accessible tissue: Callus, score: 20.931 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1218136630 | NA | 4.96E-06 | Awn_length | Ind_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1218136630 | 6.82E-06 | 2.66E-07 | mr1129 | 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 |
| vg1218136630 | 1.53E-06 | 3.72E-08 | mr1257 | 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 |