| Variant ID: vg0604842468 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 4842468 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GAAAAGATGGGGATGTTTTCTGTTCAAAGTGCATATAAAATCGCGCTTGCTGAACAACTCAGGAAAGATGATCACGGCGCAAGTAGCGCGACAGGAAACG[G/A]
GGAAAGAGCACTTTGGAAACATATATGGTCTTTTCTCTCAAAAAAAAAACATATATGGTCAGCTAATGTTCCTCAGAAAGTCCGTATTTTTGCTTGGCGT
ACGCCAAGCAAAAATACGGACTTTCTGAGGAACATTAGCTGACCATATATGTTTTTTTTTTGAGAGAAAAGACCATATATGTTTCCAAAGTGCTCTTTCC[C/T]
CGTTTCCTGTCGCGCTACTTGCGCCGTGATCATCTTTCCTGAGTTGTTCAGCAAGCGCGATTTTATATGCACTTTGAACAGAAAACATCCCCATCTTTTC
| 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 | 61.60% | 1.00% | 2.98% | 34.47% | NA |
| All Indica | 2759 | 72.60% | 0.60% | 2.10% | 24.68% | NA |
| All Japonica | 1512 | 54.30% | 1.30% | 4.10% | 40.28% | NA |
| Aus | 269 | 5.90% | 3.30% | 3.35% | 87.36% | NA |
| Indica I | 595 | 54.50% | 1.00% | 5.88% | 38.66% | NA |
| Indica II | 465 | 70.30% | 0.20% | 1.08% | 28.39% | NA |
| Indica III | 913 | 84.80% | 0.70% | 0.33% | 14.24% | NA |
| Indica Intermediate | 786 | 73.70% | 0.40% | 1.91% | 24.05% | NA |
| Temperate Japonica | 767 | 83.70% | 0.10% | 4.17% | 11.99% | NA |
| Tropical Japonica | 504 | 16.90% | 2.20% | 3.97% | 76.98% | NA |
| Japonica Intermediate | 241 | 39.00% | 3.30% | 4.15% | 53.53% | NA |
| VI/Aromatic | 96 | 21.90% | 2.10% | 6.25% | 69.79% | NA |
| Intermediate | 90 | 52.20% | 0.00% | 6.67% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0604842468 | G -> A | LOC_Os06g09530.1 | missense_variant ; p.Gly32Glu; MODERATE | nonsynonymous_codon ; G32E | Average:50.516; most accessible tissue: Callus, score: 76.332 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0604842468 | G -> DEL | LOC_Os06g09530.1 | N | frameshift_variant | Average:50.516; most accessible tissue: Callus, score: 76.332 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0604842468 | 7.32E-06 | 9.90E-07 | mr1432 | 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 |
| vg0604842468 | 6.23E-06 | 6.22E-06 | mr1939 | 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 |
| vg0604842468 | 2.98E-06 | 2.98E-06 | mr1941 | 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 |
| vg0604842468 | NA | 6.66E-06 | mr1170_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 |
| vg0604842468 | NA | 6.62E-06 | mr1754_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 |