| Variant ID: vg0403668748 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 3668748 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCTCTGCGAGCAGCGCTTCTGCGTCATCATCATCCTCCACCAGGTCCACCCGAGGTGCTTCAAGCATGATCTCCACCAAGCTTCTATACCGCACCGGCCC[G/A]
TCGTCACTGCCGGGCGTGCGCGGTGACGCCTGCACCTCGGCAGAGTGCGTTGAGGATGAGCCGAGTGTAGGCGTGCTAGGCAAGGTTGGTGAGAACCTCG
CGAGGTTCTCACCAACCTTGCCTAGCACGCCTACACTCGGCTCATCCTCAACGCACTCTGCCGAGGTGCAGGCGTCACCGCGCACGCCCGGCAGTGACGA[C/T]
GGGCCGGTGCGGTATAGAAGCTTGGTGGAGATCATGCTTGAAGCACCTCGGGTGGACCTGGTGGAGGATGATGATGACGCAGAAGCGCTGCTCGCAGAGA
| 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 | 72.90% | 19.70% | 1.40% | 6.01% | NA |
| All Indica | 2759 | 66.80% | 22.50% | 1.59% | 9.13% | NA |
| All Japonica | 1512 | 91.50% | 5.80% | 0.99% | 1.79% | NA |
| Aus | 269 | 50.90% | 46.80% | 1.49% | 0.74% | NA |
| Indica I | 595 | 95.50% | 3.70% | 0.17% | 0.67% | NA |
| Indica II | 465 | 68.00% | 26.20% | 3.66% | 2.15% | NA |
| Indica III | 913 | 48.50% | 30.20% | 1.20% | 20.04% | NA |
| Indica Intermediate | 786 | 65.50% | 25.60% | 1.91% | 7.00% | NA |
| Temperate Japonica | 767 | 96.00% | 0.30% | 0.26% | 3.52% | NA |
| Tropical Japonica | 504 | 82.50% | 15.50% | 1.98% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.90% | 2.90% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 19.80% | 79.20% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 71.10% | 23.30% | 2.22% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0403668748 | G -> DEL | LOC_Os04g06960.1 | N | frameshift_variant | Average:30.867; most accessible tissue: Zhenshan97 root, score: 64.819 | N | N | N | N |
| vg0403668748 | G -> A | LOC_Os04g06960.1 | synonymous_variant ; p.Asp687Asp; LOW | synonymous_codon | Average:30.867; most accessible tissue: Zhenshan97 root, score: 64.819 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0403668748 | NA | 8.81E-06 | mr1339 | 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 |
| vg0403668748 | 1.13E-06 | 8.59E-06 | mr1884 | 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 |
| vg0403668748 | 2.23E-06 | NA | mr1898 | 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 |