| Variant ID: vg0207793784 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 7793784 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGACCGTGGTATAGATCTGGAGGAACTCGGAGGGATTGATGTTACCATCATACTTCTCCGTAAGGTTAGGGCGAAACTTCAGGGGCCACCGAACATTCCA[G/A]
AGACTCGCCACGAAGGCCCTACAACCTGTCCCCCCAGGGGTGAGTGTGGGAGGAGGACCGCCTCGTGAGGAAGAATGTGGCGCTCCAGACGAGGAGGCGC
GCGCCTCCTCGTCTGGAGCGCCACATTCTTCCTCACGAGGCGGTCCTCCTCCCACACTCACCCCTGGGGGGACAGGTTGTAGGGCCTTCGTGGCGAGTCT[C/T]
TGGAATGTTCGGTGGCCCCTGAAGTTTCGCCCTAACCTTACGGAGAAGTATGATGGTAACATCAATCCCTCCGAGTTCCTCCAGATCTATACCACGGTCA
| 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 | 41.50% | 7.70% | 1.06% | 49.70% | NA |
| All Indica | 2759 | 13.70% | 2.10% | 1.74% | 82.49% | NA |
| All Japonica | 1512 | 97.40% | 0.30% | 0.00% | 2.38% | NA |
| Aus | 269 | 12.30% | 87.00% | 0.37% | 0.37% | NA |
| Indica I | 595 | 3.40% | 0.30% | 0.84% | 95.46% | NA |
| Indica II | 465 | 5.40% | 1.30% | 1.94% | 91.40% | NA |
| Indica III | 913 | 23.90% | 2.30% | 1.42% | 72.40% | NA |
| Indica Intermediate | 786 | 14.60% | 3.60% | 2.67% | 79.13% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.00% | 1.69% | NA |
| Tropical Japonica | 504 | 96.00% | 0.00% | 0.00% | 3.97% | NA |
| Japonica Intermediate | 241 | 97.10% | 1.70% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 41.70% | 58.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 42.20% | 16.70% | 1.11% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0207793784 | G -> A | LOC_Os02g14220.1 | synonymous_variant ; p.Leu239Leu; LOW | synonymous_codon | Average:12.962; most accessible tissue: Callus, score: 51.666 | N | N | N | N |
| vg0207793784 | G -> DEL | LOC_Os02g14220.1 | N | frameshift_variant | Average:12.962; most accessible tissue: Callus, score: 51.666 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0207793784 | 1.36E-06 | NA | mr1023 | 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 |
| vg0207793784 | NA | 7.44E-06 | mr1344_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 |
| vg0207793784 | NA | 1.84E-06 | mr1522_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 |