| Variant ID: vg0718982411 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 18982411 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 65. )
TCGTCTTCCACTTCATCTTCTTCCATTTCAACACCTTGCTCTCCGTGGGATGTCCAACAGTTATAGCTTGGCATGAACCCCGACTTAAACAAGTGGAAAT[G/A]
AATAGTCCTAGATGCAGAATACTCCTTCTGATTCTTACACTTATTGCATGGACAACAAATAAAACCCCCTTTGCCTGTTAGCTTCGGCCACTCTCAAAAA
TTTTTGAGAGTGGCCGAAGCTAACAGGCAAAGGGGGTTTTATTTGTTGTCCATGCAATAAGTGTAAGAATCAGAAGGAGTATTCTGCATCTAGGACTATT[C/T]
ATTTCCACTTGTTTAAGTCGGGGTTCATGCCAAGCTATAACTGTTGGACATCCCACGGAGAGCAAGGTGTTGAAATGGAAGAAGATGAAGTGGAAGACGA
| 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 | 76.90% | 18.00% | 1.48% | 3.58% | NA |
| All Indica | 2759 | 63.10% | 29.00% | 1.96% | 5.87% | NA |
| All Japonica | 1512 | 99.40% | 0.10% | 0.07% | 0.40% | NA |
| Aus | 269 | 80.30% | 14.90% | 4.83% | 0.00% | NA |
| Indica I | 595 | 23.40% | 71.10% | 3.36% | 2.18% | NA |
| Indica II | 465 | 76.80% | 21.70% | 1.51% | 0.00% | NA |
| Indica III | 913 | 82.40% | 7.80% | 0.66% | 9.20% | NA |
| Indica Intermediate | 786 | 62.80% | 26.20% | 2.67% | 8.27% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.60% | 0.00% | 0.20% | 1.19% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 11.10% | 2.22% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0718982411 | G -> DEL | N | N | silent_mutation | Average:14.181; most accessible tissue: Minghui63 young leaf, score: 20.156 | N | N | N | N |
| vg0718982411 | G -> A | LOC_Os07g31910.1 | upstream_gene_variant ; 4230.0bp to feature; MODIFIER | silent_mutation | Average:14.181; most accessible tissue: Minghui63 young leaf, score: 20.156 | N | N | N | N |
| vg0718982411 | G -> A | LOC_Os07g31920.1 | upstream_gene_variant ; 75.0bp to feature; MODIFIER | silent_mutation | Average:14.181; most accessible tissue: Minghui63 young leaf, score: 20.156 | N | N | N | N |
| vg0718982411 | G -> A | LOC_Os07g31920-LOC_Os07g31930 | intergenic_region ; MODIFIER | silent_mutation | Average:14.181; most accessible tissue: Minghui63 young leaf, score: 20.156 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0718982411 | NA | 6.50E-06 | mr1164_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 |
| vg0718982411 | 8.93E-07 | NA | mr1246_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 |
| vg0718982411 | 8.73E-06 | NA | mr1437_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 |
| vg0718982411 | NA | 1.38E-06 | mr1943_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 |