| Variant ID: vg0622377373 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 22377373 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTATAGCTAACACATAATCGGCGAGATGATCCTTGAGGACAGAGGACGAACACTCACTCTAGTTGGTCGAGCAGCAGGCAGCGGCTCTTTGAGTCTTTGA[C/T]
GCTGACGAGGACGAGATCGGCGAGATGATCAGATGAACGTCGATCGTCGAAGTCGAACGCCGGCGAGGCAGGCAGGCAGCCACGATCGTCGCACGCGCAG
CTGCGCGTGCGACGATCGTGGCTGCCTGCCTGCCTCGCCGGCGTTCGACTTCGACGATCGACGTTCATCTGATCATCTCGCCGATCTCGTCCTCGTCAGC[G/A]
TCAAAGACTCAAAGAGCCGCTGCCTGCTGCTCGACCAACTAGAGTGAGTGTTCGTCCTCTGTCCTCAAGGATCATCTCGCCGATTATGTGTTAGCTATAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 89.20% | 0.30% | 3.00% | 7.49% | NA |
| All Indica | 2759 | 91.00% | 0.50% | 4.68% | 3.84% | NA |
| All Japonica | 1512 | 83.90% | 0.00% | 0.53% | 15.61% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.00% | 0.74% | NA |
| Indica I | 595 | 87.20% | 1.00% | 10.42% | 1.34% | NA |
| Indica II | 465 | 83.40% | 0.00% | 6.24% | 10.32% | NA |
| Indica III | 913 | 97.30% | 0.00% | 1.10% | 1.64% | NA |
| Indica Intermediate | 786 | 91.00% | 1.00% | 3.56% | 4.45% | NA |
| Temperate Japonica | 767 | 80.80% | 0.00% | 0.78% | 18.38% | NA |
| Tropical Japonica | 504 | 85.70% | 0.00% | 0.20% | 14.09% | NA |
| Japonica Intermediate | 241 | 89.60% | 0.00% | 0.41% | 9.96% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 82.20% | 1.10% | 5.56% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0622377373 | C -> T | LOC_Os06g37820.1 | missense_variant ; p.Val611Ile; MODERATE | nonsynonymous_codon ; V611I | Average:40.05; most accessible tissue: Zhenshan97 flag leaf, score: 69.147 | unknown | unknown | TOLERATED | 0.37 |
| vg0622377373 | C -> DEL | LOC_Os06g37820.1 | N | frameshift_variant | Average:40.05; most accessible tissue: Zhenshan97 flag leaf, score: 69.147 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0622377373 | NA | 1.01E-06 | mr1669 | 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 |
| vg0622377373 | 4.25E-06 | 4.25E-06 | mr1674 | 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 |