| Variant ID: vg0729682097 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 29682097 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTCATTAAGCAGTCAGTATTCATTGCATTGTAATTTGTATAAAGTAATGTGATTAGTGGTGTGCATGTGCATGAATACATAAGCAGAAGGGAGCAGGAGG[G/A]
CTACTTGAGGCATTGTTTGGTTTGTGAGGGGAACTAATCCCTTAGGGGATAAAATCCCCCACAGATTGTTTGGATACAACTATTGAGAAGGGGGGGGTCA
TGACCCCCCCCTTCTCAATAGTTGTATCCAAACAATCTGTGGGGGATTTTATCCCCTAAGGGATTAGTTCCCCTCACAAACCAAACAATGCCTCAAGTAG[C/T]
CCTCCTGCTCCCTTCTGCTTATGTATTCATGCACATGCACACCACTAATCACATTACTTTATACAAATTACAATGCAATGAATACTGACTGCTTAATGAA
| 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 | 38.30% | 12.60% | 0.23% | 48.79% | NA |
| All Indica | 2759 | 8.40% | 21.30% | 0.40% | 69.84% | NA |
| All Japonica | 1512 | 87.00% | 0.30% | 0.00% | 12.70% | NA |
| Aus | 269 | 42.80% | 0.00% | 0.00% | 57.25% | NA |
| Indica I | 595 | 2.00% | 4.40% | 1.18% | 92.44% | NA |
| Indica II | 465 | 4.50% | 10.10% | 0.22% | 85.16% | NA |
| Indica III | 913 | 11.60% | 37.00% | 0.00% | 51.37% | NA |
| Indica Intermediate | 786 | 12.00% | 22.50% | 0.38% | 65.14% | NA |
| Temperate Japonica | 767 | 99.10% | 0.00% | 0.00% | 0.91% | NA |
| Tropical Japonica | 504 | 77.80% | 0.80% | 0.00% | 21.43% | NA |
| Japonica Intermediate | 241 | 68.00% | 0.00% | 0.00% | 31.95% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 62.20% | 5.60% | 0.00% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0729682097 | G -> DEL | N | N | silent_mutation | Average:10.872; most accessible tissue: Callus, score: 61.829 | N | N | N | N |
| vg0729682097 | G -> A | LOC_Os07g49540.1 | upstream_gene_variant ; 1823.0bp to feature; MODIFIER | silent_mutation | Average:10.872; most accessible tissue: Callus, score: 61.829 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0729682097 | 4.69E-06 | NA | mr1119 | 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 |
| vg0729682097 | NA | 1.01E-07 | mr1716 | 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 |