| Variant ID: vg0206556033 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 6556033 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGAATTGTTTAGAGAAGCTTCCGATTAAAAAGAAGCTACAGCTGTAAGAAGTTTTCCAAACAAACCATTCATCTCTCTCTTTGCTTGCTAGCCATGGATG[G/A]
GCTCTTGTACCAAGCGCTCCTCCTCTCCGCGCTCGCCGTCGCGGTGCTCCAGATCGTCAAGCTCGCCGTCGTCAACAGAGGGAAGAAGCAAGCGGCGGCG
CGCCGCCGCTTGCTTCTTCCCTCTGTTGACGACGGCGAGCTTGACGATCTGGAGCACCGCGACGGCGAGCGCGGAGAGGAGGAGCGCTTGGTACAAGAGC[C/T]
CATCCATGGCTAGCAAGCAAAGAGAGAGATGAATGGTTTGTTTGGAAAACTTCTTACAGCTGTAGCTTCTTTTTAATCGGAAGCTTCTCTAAACAATTCA
| 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 | 85.10% | 2.80% | 2.88% | 9.25% | NA |
| All Indica | 2759 | 82.40% | 2.00% | 4.31% | 11.31% | NA |
| All Japonica | 1512 | 98.40% | 0.30% | 0.99% | 0.33% | NA |
| Aus | 269 | 48.30% | 25.70% | 0.00% | 26.02% | NA |
| Indica I | 595 | 68.10% | 5.00% | 8.07% | 18.82% | NA |
| Indica II | 465 | 97.40% | 0.00% | 1.08% | 1.51% | NA |
| Indica III | 913 | 89.00% | 0.50% | 2.30% | 8.11% | NA |
| Indica Intermediate | 786 | 76.60% | 2.50% | 5.73% | 15.14% | NA |
| Temperate Japonica | 767 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 97.40% | 0.00% | 2.38% | 0.20% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 1.24% | 1.66% | NA |
| VI/Aromatic | 96 | 54.20% | 1.00% | 0.00% | 44.79% | NA |
| Intermediate | 90 | 88.90% | 1.10% | 2.22% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0206556033 | G -> A | LOC_Os02g12540.1 | missense_variant ; p.Gly3Glu; MODERATE | nonsynonymous_codon ; G3E | Average:30.861; most accessible tissue: Minghui63 flag leaf, score: 63.692 | unknown | unknown | TOLERATED | 1.00 |
| vg0206556033 | G -> DEL | LOC_Os02g12540.1 | N | frameshift_variant | Average:30.861; most accessible tissue: Minghui63 flag leaf, score: 63.692 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0206556033 | 1.27E-07 | NA | mr1068_2 | 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 |
| vg0206556033 | 5.78E-08 | NA | mr1090_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 |
| vg0206556033 | NA | 1.64E-08 | mr1126_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 |
| vg0206556033 | 5.39E-06 | NA | mr1200_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 |
| vg0206556033 | 4.92E-07 | NA | mr1211_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 |
| vg0206556033 | NA | 9.57E-07 | mr1567_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 |
| vg0206556033 | NA | 2.87E-06 | mr1574_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 |