| Variant ID: vg0206207021 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 6207021 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TAAGGGTTTATTTGGGGGAGCTTTAAATTTTGAGAAGCAGCTGTTTGGTAGCCAGCTTCTGAGAATCTGGAAAAGCTCTGAAACCTAGCTTTTATATCTT[C/A]
TGGCTTTTTAGTTCATTTTTCAGAATCTTAGACTGTTTGGGGCAGCTTCTAGCAGAAGCAGCTTTTAGGAAAAGCTGCAGCTGGGACAAACTCTCCCAAA
TTTGGGAGAGTTTGTCCCAGCTGCAGCTTTTCCTAAAAGCTGCTTCTGCTAGAAGCTGCCCCAAACAGTCTAAGATTCTGAAAAATGAACTAAAAAGCCA[G/T]
AAGATATAAAAGCTAGGTTTCAGAGCTTTTCCAGATTCTCAGAAGCTGGCTACCAAACAGCTGCTTCTCAAAATTTAAAGCTCCCCCAAATAAACCCTTA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 53.30% | 2.90% | 4.30% | 39.48% | NA |
| All Indica | 2759 | 40.70% | 0.00% | 4.60% | 54.73% | NA |
| All Japonica | 1512 | 84.90% | 9.10% | 4.10% | 1.92% | NA |
| Aus | 269 | 3.30% | 0.00% | 2.60% | 94.05% | NA |
| Indica I | 595 | 21.70% | 0.00% | 1.34% | 76.97% | NA |
| Indica II | 465 | 28.00% | 0.00% | 7.96% | 64.09% | NA |
| Indica III | 913 | 56.00% | 0.00% | 4.93% | 39.10% | NA |
| Indica Intermediate | 786 | 44.80% | 0.00% | 4.71% | 50.51% | NA |
| Temperate Japonica | 767 | 79.80% | 11.60% | 6.65% | 1.96% | NA |
| Tropical Japonica | 504 | 96.00% | 1.80% | 0.99% | 1.19% | NA |
| Japonica Intermediate | 241 | 78.00% | 16.20% | 2.49% | 3.32% | NA |
| VI/Aromatic | 96 | 55.20% | 0.00% | 3.12% | 41.67% | NA |
| Intermediate | 90 | 57.80% | 0.00% | 4.44% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0206207021 | C -> A | LOC_Os02g11970.1 | 3_prime_UTR_variant ; 111.0bp to feature; MODIFIER | silent_mutation | Average:35.225; most accessible tissue: Callus, score: 79.446 | N | N | N | N |
| vg0206207021 | C -> A | LOC_Os02g11970.2 | 3_prime_UTR_variant ; 111.0bp to feature; MODIFIER | silent_mutation | Average:35.225; most accessible tissue: Callus, score: 79.446 | N | N | N | N |
| vg0206207021 | C -> A | LOC_Os02g11960.1 | downstream_gene_variant ; 2647.0bp to feature; MODIFIER | silent_mutation | Average:35.225; most accessible tissue: Callus, score: 79.446 | N | N | N | N |
| vg0206207021 | C -> A | LOC_Os02g11980.1 | downstream_gene_variant ; 1663.0bp to feature; MODIFIER | silent_mutation | Average:35.225; most accessible tissue: Callus, score: 79.446 | N | N | N | N |
| vg0206207021 | C -> DEL | N | N | silent_mutation | Average:35.225; most accessible tissue: Callus, score: 79.446 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0206207021 | NA | 9.18E-06 | mr1324 | 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 |
| vg0206207021 | 8.03E-07 | 8.03E-07 | mr1803 | 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 |
| vg0206207021 | NA | 9.50E-06 | mr1456_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 |