| Variant ID: vg1017284750 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 17284750 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGACGTCGTCGGTGATGTCGGAGATCTTGTTGCGTTGTTCAGAGAAGCGTCGGATGTAATCTCGAAGGGATTCTCCAGACTTCTGAACGATGTTGTAGAG[G/A]
TCAAATTGTGTGCCGGGGCGCTCAAAGGTGCCCTGGAAGTTGGCGATGAAGTGATCGCGAAGTTCCGCCCATGATCCGATCGTGCGACGGGGTAGTCCGT
ACGGACTACCCCGTCGCACGATCGGATCATGGGCGGAACTTCGCGATCACTTCATCGCCAACTTCCAGGGCACCTTTGAGCGCCCCGGCACACAATTTGA[C/T]
CTCTACAACATCGTTCAGAAGTCTGGAGAATCCCTTCGAGATTACATCCGACGCTTCTCTGAACAACGCAACAAGATCTCCGACATCACCGACGACGTCA
| 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 | 85.80% | 13.30% | 0.80% | 0.04% | NA |
| All Indica | 2759 | 76.20% | 22.40% | 1.34% | 0.07% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| Indica II | 465 | 83.20% | 16.30% | 0.43% | 0.00% | NA |
| Indica III | 913 | 59.00% | 37.70% | 3.29% | 0.00% | NA |
| Indica Intermediate | 786 | 75.70% | 23.40% | 0.64% | 0.25% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 7.80% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1017284750 | G -> A | LOC_Os10g33010.1 | synonymous_variant ; p.Asp434Asp; LOW | synonymous_codon | Average:46.64; most accessible tissue: Zhenshan97 panicle, score: 71.253 | N | N | N | N |
| vg1017284750 | G -> DEL | LOC_Os10g33010.1 | N | frameshift_variant | Average:46.64; most accessible tissue: Zhenshan97 panicle, score: 71.253 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1017284750 | NA | 7.49E-06 | mr1124 | 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 |
| vg1017284750 | 2.81E-07 | NA | mr1970 | 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 |
| vg1017284750 | NA | 6.90E-07 | mr1970 | 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 |
| vg1017284750 | 3.69E-06 | NA | mr1973 | 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 |