| Variant ID: vg0907667465 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 7667465 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TAGAAAAACAAATCCTACTGAAAAAAGTAAAAATAAAATAACAGATGAAAAAAACCGAAAAAAGGAGGAAAAGGTGAAAATTTTGGATGGAAAAAATAGA[G/C]
GGACGGAGAGAAACGGAAAAATAAGCGGGCAGAGAAAAAAAAAGGAAAAAAGGGCGAGAAAAAATGGGAAACAAAGTGGACGGAAAGAAAGGAAAAAACA
TGTTTTTTCCTTTCTTTCCGTCCACTTTGTTTCCCATTTTTTCTCGCCCTTTTTTCCTTTTTTTTTCTCTGCCCGCTTATTTTTCCGTTTCTCTCCGTCC[C/G]
TCTATTTTTTCCATCCAAAATTTTCACCTTTTCCTCCTTTTTTCGGTTTTTTTCATCTGTTATTTTATTTTTACTTTTTTCAGTAGGATTTGTTTTTCTA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.30% | 13.80% | 0.28% | 56.60% | NA |
| All Indica | 2759 | 11.00% | 7.50% | 0.33% | 81.12% | NA |
| All Japonica | 1512 | 59.30% | 28.20% | 0.20% | 12.30% | NA |
| Aus | 269 | 16.40% | 1.50% | 0.00% | 82.16% | NA |
| Indica I | 595 | 15.00% | 3.00% | 0.17% | 81.85% | NA |
| Indica II | 465 | 7.70% | 2.60% | 0.65% | 89.03% | NA |
| Indica III | 913 | 8.20% | 14.00% | 0.11% | 77.66% | NA |
| Indica Intermediate | 786 | 13.20% | 6.40% | 0.51% | 79.90% | NA |
| Temperate Japonica | 767 | 56.30% | 21.60% | 0.26% | 21.77% | NA |
| Tropical Japonica | 504 | 75.40% | 23.00% | 0.20% | 1.39% | NA |
| Japonica Intermediate | 241 | 35.30% | 59.80% | 0.00% | 4.98% | NA |
| VI/Aromatic | 96 | 94.80% | 1.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 56.70% | 13.30% | 1.11% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0907667465 | G -> DEL | N | N | silent_mutation | Average:8.189; most accessible tissue: Callus, score: 42.434 | N | N | N | N |
| vg0907667465 | G -> C | LOC_Os09g13290.1 | downstream_gene_variant ; 3637.0bp to feature; MODIFIER | silent_mutation | Average:8.189; most accessible tissue: Callus, score: 42.434 | N | N | N | N |
| vg0907667465 | G -> C | LOC_Os09g13300.1 | downstream_gene_variant ; 3238.0bp to feature; MODIFIER | silent_mutation | Average:8.189; most accessible tissue: Callus, score: 42.434 | N | N | N | N |
| vg0907667465 | G -> C | LOC_Os09g13290-LOC_Os09g13300 | intergenic_region ; MODIFIER | silent_mutation | Average:8.189; most accessible tissue: Callus, score: 42.434 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0907667465 | 5.51E-06 | 5.51E-06 | mr1427_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 |
| vg0907667465 | NA | 4.05E-07 | mr1633_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 |
| vg0907667465 | 6.11E-06 | NA | mr1633_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 |
| vg0907667465 | 2.36E-06 | NA | mr1754_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 |