| Variant ID: vg0711374428 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 11374428 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CATGATCAGTTCTTGAGGCCTCGGGTCACCCCGGATCCCCGGTTTCACACCGTTTTCCAGAAGACAGTGTATGAGCAGGTTTATGTAGGGAAAGCTTTTG[C/T]
AGAGTATAAGTGGATTTCTTGGAGAGACATCAATGAGACTCCAGAGTTTAAGAGCTTGCAGGATCTCTTCAAGACTGTTGGCATTGACCGGATTGTGACC
GGTCACAATCCGGTCAATGCCAACAGTCTTGAAGAGATCCTGCAAGCTCTTAAACTCTGGAGTCTCATTGATGTCTCTCCAAGAAATCCACTTATACTCT[G/A]
CAAAAGCTTTCCCTACATAAACCTGCTCATACACTGTCTTCTGGAAAACGGTGTGAAACCGGGGATCCGGGGTGACCCGAGGCCTCAAGAACTGATCATG
| 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 | 54.90% | 26.00% | 1.42% | 17.63% | NA |
| All Indica | 2759 | 89.30% | 1.70% | 1.56% | 7.39% | NA |
| All Japonica | 1512 | 0.90% | 75.30% | 0.60% | 23.21% | NA |
| Aus | 269 | 28.30% | 1.90% | 3.72% | 66.17% | NA |
| Indica I | 595 | 92.40% | 1.30% | 1.85% | 4.37% | NA |
| Indica II | 465 | 83.70% | 4.10% | 1.94% | 10.32% | NA |
| Indica III | 913 | 93.80% | 0.30% | 1.10% | 4.82% | NA |
| Indica Intermediate | 786 | 85.10% | 2.30% | 1.65% | 10.94% | NA |
| Temperate Japonica | 767 | 0.70% | 65.60% | 0.78% | 32.99% | NA |
| Tropical Japonica | 504 | 0.60% | 88.30% | 0.40% | 10.71% | NA |
| Japonica Intermediate | 241 | 2.10% | 79.30% | 0.41% | 18.26% | NA |
| VI/Aromatic | 96 | 12.50% | 1.00% | 2.08% | 84.38% | NA |
| Intermediate | 90 | 34.40% | 41.10% | 3.33% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0711374428 | C -> DEL | LOC_Os07g19200.1 | N | frameshift_variant | Average:16.694; most accessible tissue: Callus, score: 42.522 | N | N | N | N |
| vg0711374428 | C -> T | LOC_Os07g19200.1 | missense_variant ; p.Ala1005Val; MODERATE | nonsynonymous_codon ; A1005V | Average:16.694; most accessible tissue: Callus, score: 42.522 | unknown | unknown | TOLERATED | 0.08 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0711374428 | NA | 3.68E-07 | mr1554 | 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 |
| vg0711374428 | 3.31E-06 | 5.01E-06 | mr1928 | 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 |