| Variant ID: vg0617685840 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 17685840 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 259. )
CGAACGAACATGAACGAGAACAAGGTGAATGAACGTGAACGAGAACGTTGTCGGACGAACGTGAACGAGCCAACGAACGTGAACGTGAAATGCAATTATA[C/G]
GCAGGTTAATGAACGTGAACGAACAAACGTAGGTGAATGAAACGTGACCTTAACGAGAACGCGAACGTGAACGATATCGTGAACGAAACGTGAACGTCAA
TTGACGTTCACGTTTCGTTCACGATATCGTTCACGTTCGCGTTCTCGTTAAGGTCACGTTTCATTCACCTACGTTTGTTCGTTCACGTTCATTAACCTGC[G/C]
TATAATTGCATTTCACGTTCACGTTCGTTGGCTCGTTCACGTTCGTCCGACAACGTTCTCGTTCACGTTCATTCACCTTGTTCTCGTTCATGTTCGTTCG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.70% | 1.70% | 20.72% | 44.88% | NA |
| All Indica | 2759 | 3.70% | 2.50% | 27.36% | 66.44% | NA |
| All Japonica | 1512 | 93.00% | 0.30% | 1.85% | 4.83% | NA |
| Aus | 269 | 0.40% | 1.90% | 40.89% | 56.88% | NA |
| Indica I | 595 | 4.50% | 0.70% | 16.47% | 78.32% | NA |
| Indica II | 465 | 4.10% | 2.20% | 8.82% | 84.95% | NA |
| Indica III | 913 | 1.00% | 4.10% | 42.72% | 52.25% | NA |
| Indica Intermediate | 786 | 6.00% | 2.30% | 28.75% | 62.98% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 0.13% | 3.39% | NA |
| Tropical Japonica | 504 | 85.90% | 1.00% | 4.76% | 8.33% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.00% | 1.24% | 2.07% | NA |
| VI/Aromatic | 96 | 1.00% | 1.00% | 76.04% | 21.88% | NA |
| Intermediate | 90 | 38.90% | 1.10% | 14.44% | 45.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0617685840 | C -> G | LOC_Os06g30570.1 | missense_variant ; p.Thr55Arg; MODERATE | nonsynonymous_codon ; T55R | Average:13.016; most accessible tissue: Callus, score: 19.449 | unknown | unknown | TOLERATED | 0.33 |
| vg0617685840 | C -> DEL | LOC_Os06g30570.1 | N | frameshift_variant | Average:13.016; most accessible tissue: Callus, score: 19.449 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0617685840 | NA | 1.34E-06 | mr1014 | 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 |
| vg0617685840 | NA | 5.81E-06 | mr1298 | 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 |
| vg0617685840 | 8.60E-06 | 7.65E-08 | mr1706 | 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 |
| vg0617685840 | NA | 8.66E-08 | mr1706 | 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 |
| vg0617685840 | NA | 3.00E-07 | mr1835 | 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 |
| vg0617685840 | 7.82E-06 | 2.72E-07 | mr1835 | 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 |
| vg0617685840 | NA | 4.71E-06 | mr1931_2 | 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 |