| Variant ID: vg0116961602 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 16961602 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TTAGCAGTGCAGTAGGTGGCCGAATCGGATTCCAGCATTTGGAGGCCTTGACCTTGATGTCTTCTTGTTCATCTATGATGTGAGCAATGGTTGTATCCAT[A/G]
GTAGCTATGGTCACATCACAAAGGCTAGTGGGCCCCACAGGTTAGTTTTGACCGTTGTGGATGCACTATTTAAGCCAACCGGCCGGGAGAGGGGACTCCA
TGGAGTCCCCTCTCCCGGCCGGTTGGCTTAAATAGTGCATCCACAACGGTCAAAACTAACCTGTGGGGCCCACTAGCCTTTGTGATGTGACCATAGCTAC[T/C]
ATGGATACAACCATTGCTCACATCATAGATGAACAAGAAGACATCAAGGTCAAGGCCTCCAAATGCTGGAATCCGATTCGGCCACCTACTGCACTGCTAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 41.60% | 0.40% | 1.50% | 56.43% | NA |
| All Indica | 2759 | 9.00% | 0.70% | 2.25% | 88.08% | NA |
| All Japonica | 1512 | 97.40% | 0.00% | 0.07% | 2.51% | NA |
| Aus | 269 | 37.20% | 0.00% | 2.60% | 60.22% | NA |
| Indica I | 595 | 10.30% | 0.30% | 2.35% | 87.06% | NA |
| Indica II | 465 | 11.60% | 0.00% | 2.37% | 86.02% | NA |
| Indica III | 913 | 3.60% | 1.00% | 2.41% | 92.99% | NA |
| Indica Intermediate | 786 | 12.60% | 1.10% | 1.91% | 84.35% | NA |
| Temperate Japonica | 767 | 99.10% | 0.00% | 0.13% | 0.78% | NA |
| Tropical Japonica | 504 | 94.60% | 0.00% | 0.00% | 5.36% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 93.80% | 0.00% | 0.00% | 6.25% | NA |
| Intermediate | 90 | 64.40% | 0.00% | 1.11% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0116961602 | A -> G | LOC_Os01g31020.1 | missense_variant ; p.Ser50Gly; MODERATE | nonsynonymous_codon ; S50G | Average:8.51; most accessible tissue: Callus, score: 32.991 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0116961602 | A -> DEL | LOC_Os01g31020.1 | N | frameshift_variant | Average:8.51; most accessible tissue: Callus, score: 32.991 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0116961602 | 3.31E-06 | 3.31E-06 | mr1049_2 | 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 |
| vg0116961602 | 2.38E-06 | 2.38E-06 | mr1344_2 | 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 |
| vg0116961602 | 5.35E-06 | NA | mr1817_2 | Ind_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 |
| vg0116961602 | 1.33E-06 | 1.33E-06 | mr1981_2 | 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 |