| Variant ID: vg0716335933 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 16335933 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.77, G: 0.23, others allele: 0.00, population size: 227. )
TGGAAGAAAGAACAATTAAAATGCTGACTGACGGGCCATCAAGTGTGTATACCTTGTGGCAAGCATATGATCTGAATGGATACACGTTTTACACAAAAGC[A/G]
AAAGACAAAAGGAGTGCATGCCAAAACAGTGGCATTCGAGTAGAAGCAATCGACACAACTGGGCAAAAGAGCACATACTATGGATTCATAGAAAAAATCT
AGATTTTTTCTATGAATCCATAGTATGTGCTCTTTTGCCCAGTTGTGTCGATTGCTTCTACTCGAATGCCACTGTTTTGGCATGCACTCCTTTTGTCTTT[T/C]
GCTTTTGTGTAAAACGTGTATCCATTCAGATCATATGCTTGCCACAAGGTATACACACTTGATGGCCCGTCAGTCAGCATTTTAATTGTTCTTTCTTCCA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 70.40% | 23.70% | 3.09% | 2.81% | NA |
| All Indica | 2759 | 76.40% | 21.60% | 1.63% | 0.33% | NA |
| All Japonica | 1512 | 65.50% | 30.00% | 4.56% | 0.00% | NA |
| Aus | 269 | 24.90% | 17.80% | 11.15% | 46.10% | NA |
| Indica I | 595 | 71.90% | 27.60% | 0.50% | 0.00% | NA |
| Indica II | 465 | 86.20% | 13.50% | 0.00% | 0.22% | NA |
| Indica III | 913 | 81.40% | 18.00% | 0.66% | 0.00% | NA |
| Indica Intermediate | 786 | 68.30% | 26.10% | 4.58% | 1.02% | NA |
| Temperate Japonica | 767 | 81.40% | 12.30% | 6.39% | 0.00% | NA |
| Tropical Japonica | 504 | 35.10% | 61.70% | 3.17% | 0.00% | NA |
| Japonica Intermediate | 241 | 78.40% | 19.90% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 74.40% | 24.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0716335933 | A -> DEL | LOC_Os07g28000.1 | N | frameshift_variant | Average:26.969; most accessible tissue: Minghui63 flag leaf, score: 55.781 | N | N | N | N |
| vg0716335933 | A -> G | LOC_Os07g28000.1 | synonymous_variant ; p.Ala758Ala; LOW | synonymous_codon | Average:26.969; most accessible tissue: Minghui63 flag leaf, score: 55.781 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0716335933 | NA | 9.33E-10 | mr1705 | 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 |
| vg0716335933 | NA | 8.27E-07 | mr1705 | 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 |
| vg0716335933 | 2.87E-07 | 1.93E-16 | mr1705_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 |
| vg0716335933 | 1.18E-06 | 1.03E-09 | mr1705_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 |