| Variant ID: vg1215153650 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 15153650 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TACCGTGCACTCTTTCTGGGTAGGGTTCCGTTCCACTCCAAACCTATTTGGAAGACTCCCCCCCCTCGAGATGCAGGTTCTTTGCCTAGCTGGTCACAAT[G/A]
AGGCACTGTTGGACGGCGGACTGCCTGCGTTCCAGGGGTTTGCCTCACCCGGACAGATGTGTGCTCTGTGACCAACATGATGAGACTATTGATCACATCT
AGATGTGATCAATAGTCTCATCATGTTGGTCACAGAGCACACATCTGTCCGGGTGAGGCAAACCCCTGGAACGCAGGCAGTCCGCCGTCCAACAGTGCCT[C/T]
ATTGTGACCAGCTAGGCAAAGAACCTGCATCTCGAGGGGGGGGAGTCTTCCAAATAGGTTTGGAGTGGAACGGAACCCTACCCAGAAAGAGTGCACGGTA
| 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 | 93.50% | 0.50% | 0.70% | 5.23% | NA |
| All Indica | 2759 | 90.60% | 0.00% | 0.58% | 8.81% | NA |
| All Japonica | 1512 | 97.50% | 1.70% | 0.79% | 0.07% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 99.00% | 0.00% | 0.00% | 1.01% | NA |
| Indica II | 465 | 97.00% | 0.00% | 0.00% | 3.01% | NA |
| Indica III | 913 | 82.70% | 0.00% | 0.77% | 16.54% | NA |
| Indica Intermediate | 786 | 89.70% | 0.00% | 1.15% | 9.16% | NA |
| Temperate Japonica | 767 | 95.30% | 3.10% | 1.56% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.20% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 0.00% | 4.44% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1215153650 | G -> DEL | LOC_Os12g26080.1 | N | frameshift_variant | Average:65.01; most accessible tissue: Zhenshan97 young leaf, score: 84.624 | N | N | N | N |
| vg1215153650 | G -> A | LOC_Os12g26080.1 | missense_variant ; p.His174Tyr; MODERATE | nonsynonymous_codon ; H174Y | Average:65.01; most accessible tissue: Zhenshan97 young leaf, score: 84.624 | unknown | unknown | DELETERIOUS | 0.00 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1215153650 | 1.46E-06 | 1.46E-06 | mr1108_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 |
| vg1215153650 | 1.99E-06 | 1.45E-06 | mr1112_2 | 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 |
| vg1215153650 | NA | 1.47E-07 | mr1718_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 |