| Variant ID: vg0905282574 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 5282574 |
| 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: 61. )
CCAGCAGGGAGCGCCCAACCGGCAAGTGGTGCACCGTCCACAACACCTCCCTCCACGACCTCGTGGACTGCCGCGCAGCCAAAAGTTTGGCTGAGCGGAC[G/A]
AGGAAGTGGGAGGAGGAGAGGAGGCAGGAGCGCCGAGAAGGCAAGTCCCCGGCGGTTCCCTCTGGCAATCAGCGAAGTGAGGCCAAGCAGAAGGCCCCCG
CGGGGGCCTTCTGCTTGGCCTCACTTCGCTGATTGCCAGAGGGAACCGCCGGGGACTTGCCTTCTCGGCGCTCCTGCCTCCTCTCCTCCTCCCACTTCCT[C/T]
GTCCGCTCAGCCAAACTTTTGGCTGCGCGGCAGTCCACGAGGTCGTGGAGGGAGGTGTTGTGGACGGTGCACCACTTGCCGGTTGGGCGCTCCCTGCTGG
| 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 | 56.30% | 5.80% | 12.29% | 25.65% | NA |
| All Indica | 2759 | 39.60% | 9.70% | 19.32% | 31.32% | NA |
| All Japonica | 1512 | 82.90% | 0.10% | 0.46% | 16.47% | NA |
| Aus | 269 | 91.40% | 0.00% | 5.95% | 2.60% | NA |
| Indica I | 595 | 30.40% | 0.70% | 24.37% | 44.54% | NA |
| Indica II | 465 | 40.90% | 25.20% | 12.90% | 21.08% | NA |
| Indica III | 913 | 44.70% | 7.40% | 19.39% | 28.48% | NA |
| Indica Intermediate | 786 | 39.90% | 10.20% | 19.21% | 30.66% | NA |
| Temperate Japonica | 767 | 90.40% | 0.30% | 0.26% | 9.13% | NA |
| Tropical Japonica | 504 | 84.90% | 0.00% | 0.60% | 14.48% | NA |
| Japonica Intermediate | 241 | 55.20% | 0.00% | 0.83% | 43.98% | NA |
| VI/Aromatic | 96 | 15.60% | 0.00% | 13.54% | 70.83% | NA |
| Intermediate | 90 | 58.90% | 1.10% | 13.33% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0905282574 | G -> DEL | LOC_Os09g09760.1 | N | frameshift_variant | Average:9.403; most accessible tissue: Callus, score: 23.432 | N | N | N | N |
| vg0905282574 | G -> A | LOC_Os09g09760.1 | synonymous_variant ; p.Thr385Thr; LOW | synonymous_codon | Average:9.403; most accessible tissue: Callus, score: 23.432 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0905282574 | NA | 2.33E-07 | mr1024_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 |
| vg0905282574 | 5.30E-07 | NA | mr1584_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 |
| vg0905282574 | 1.11E-07 | 1.11E-07 | mr1584_2 | 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 |
| vg0905282574 | NA | 6.06E-06 | mr1928_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 |