| Variant ID: vg0711712797 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 11712797 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATGATCAACTCGAACAGTTCGAGGAGGAGGATTTGGTTTTGCTATCTAACAGATTTTCTCGAGCTATGAAAAATGTTAGGAACAGGAAAAGAGGAGAACC[G/A]
AATCGTTGTTTTGAATGTGGAGCACTTGATCATCTTCGTTCACATTGTCCTAAGCTTGGAAGAGGAAAGAAGGAAGATGATAGTAGAGTCAAAGATGATG
CATCATCTTTGACTCTACTATCATCTTCCTTCTTTCCTCTTCCAAGCTTAGGACAATGTGAACGAAGATGATCAAGTGCTCCACATTCAAAACAACGATT[C/T]
GGTTCTCCTCTTTTCCTGTTCCTAACATTTTTCATAGCTCGAGAAAATCTGTTAGATAGCAAAACCAAATCCTCCTCCTCGAACTGTTCGAGTTGATCAT
| 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 | 80.00% | 7.20% | 4.44% | 8.36% | NA |
| All Indica | 2759 | 76.80% | 12.00% | 7.00% | 4.17% | NA |
| All Japonica | 1512 | 84.50% | 0.10% | 0.46% | 14.95% | NA |
| Aus | 269 | 97.80% | 0.40% | 0.74% | 1.12% | NA |
| Indica I | 595 | 50.60% | 22.40% | 16.13% | 10.92% | NA |
| Indica II | 465 | 86.70% | 4.50% | 6.88% | 1.94% | NA |
| Indica III | 913 | 86.70% | 12.40% | 0.88% | 0.00% | NA |
| Indica Intermediate | 786 | 79.30% | 8.30% | 7.25% | 5.22% | NA |
| Temperate Japonica | 767 | 73.80% | 0.10% | 0.39% | 25.68% | NA |
| Tropical Japonica | 504 | 99.40% | 0.20% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 87.10% | 0.00% | 1.66% | 11.20% | NA |
| VI/Aromatic | 96 | 47.90% | 0.00% | 3.12% | 48.96% | NA |
| Intermediate | 90 | 84.40% | 5.60% | 5.56% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0711712797 | G -> DEL | LOC_Os07g20300.1 | N | frameshift_variant | Average:21.836; most accessible tissue: Zhenshan97 young leaf, score: 37.835 | N | N | N | N |
| vg0711712797 | G -> A | LOC_Os07g20300.1 | synonymous_variant ; p.Pro108Pro; LOW | synonymous_codon | Average:21.836; most accessible tissue: Zhenshan97 young leaf, score: 37.835 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0711712797 | 3.95E-06 | NA | mr1349_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 |
| vg0711712797 | NA | 1.08E-10 | mr1709_2 | 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 |