| Variant ID: vg0430345493 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30345493 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 213. )
AACAACACACGATCTAGAAAGCTAACGGAACTACTCTTCTCGGAAGGATTGGGTTTGGGTCAGCTTCGGGGAAACTTCACTTGATCTTCGCGGGACGACG[A/G]
CCTTGAACTGATCTTCTCGCTCCTTGCACGAAGCTTGAGGCTTGACTTGACTTGACTCCCGAACAGACATGAAGCTGAGCCGGTCCTCTAGGTGTGACAA
TTGTCACACCTAGAGGACCGGCTCAGCTTCATGTCTGTTCGGGAGTCAAGTCAAGTCAAGCCTCAAGCTTCGTGCAAGGAGCGAGAAGATCAGTTCAAGG[T/C]
CGTCGTCCCGCGAAGATCAAGTGAAGTTTCCCCGAAGCTGACCCAAACCCAATCCTTCCGAGAAGAGTAGTTCCGTTAGCTTTCTAGATCGTGTGTTGTT
| 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 | 93.60% | 2.00% | 2.43% | 1.95% | NA |
| All Indica | 2759 | 96.60% | 0.20% | 0.11% | 3.12% | NA |
| All Japonica | 1512 | 86.80% | 5.80% | 7.28% | 0.20% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.00% | 0.74% | NA |
| Indica I | 595 | 99.50% | 0.00% | 0.00% | 0.50% | NA |
| Indica II | 465 | 98.10% | 0.40% | 0.43% | 1.08% | NA |
| Indica III | 913 | 95.10% | 0.10% | 0.11% | 4.71% | NA |
| Indica Intermediate | 786 | 95.30% | 0.30% | 0.00% | 4.45% | NA |
| Temperate Japonica | 767 | 99.10% | 0.50% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 64.30% | 15.90% | 19.84% | 0.00% | NA |
| Japonica Intermediate | 241 | 94.60% | 1.20% | 3.73% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0430345493 | A -> DEL | N | N | silent_mutation | Average:16.024; most accessible tissue: Zhenshan97 flag leaf, score: 25.809 | N | N | N | N |
| vg0430345493 | A -> G | LOC_Os04g51210.1 | upstream_gene_variant ; 586.0bp to feature; MODIFIER | silent_mutation | Average:16.024; most accessible tissue: Zhenshan97 flag leaf, score: 25.809 | N | N | N | N |
| vg0430345493 | A -> G | LOC_Os04g51220.1 | upstream_gene_variant ; 3934.0bp to feature; MODIFIER | silent_mutation | Average:16.024; most accessible tissue: Zhenshan97 flag leaf, score: 25.809 | N | N | N | N |
| vg0430345493 | A -> G | LOC_Os04g51210-LOC_Os04g51220 | intergenic_region ; MODIFIER | silent_mutation | Average:16.024; most accessible tissue: Zhenshan97 flag leaf, score: 25.809 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0430345493 | NA | 5.38E-09 | mr1040 | Jap_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 |
| vg0430345493 | 1.25E-06 | 1.25E-06 | mr1362 | Jap_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 |
| vg0430345493 | NA | 9.35E-06 | mr1362_2 | Jap_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 |