| Variant ID: vg0409847596 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9847596 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, G: 0.07, others allele: 0.00, population size: 59. )
AGGGGGACTAGGAGATTAGTGCGCGTGGCGAAAACAGTTCTGGCAGAAGGACGGCCGGTCCGCTGCCAAGGCGCGCCTTTGGGAGCAACTAGCAAAGGCG[A/G]
AGGTGGCAGACCAGTGCAAAGAAGAGGACGCAGCAGGCGAAGAGGTTGGAGGCGATGCCTAGGATCACCTAGAGGTGTGAGGCCCTCCGCCCTTTCCTTA
TAAGGAAAGGGCGGAGGGCCTCACACCTCTAGGTGATCCTAGGCATCGCCTCCAACCTCTTCGCCTGCTGCGTCCTCTTCTTTGCACTGGTCTGCCACCT[T/C]
CGCCTTTGCTAGTTGCTCCCAAAGGCGCGCCTTGGCAGCGGACCGGCCGTCCTTCTGCCAGAACTGTTTTCGCCACGCGCACTAATCTCCTAGTCCCCCT
| 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 | 30.70% | 25.80% | 3.58% | 39.93% | NA |
| All Indica | 2759 | 45.60% | 8.70% | 1.12% | 44.55% | NA |
| All Japonica | 1512 | 1.20% | 62.50% | 7.34% | 28.97% | NA |
| Aus | 269 | 49.40% | 2.20% | 4.09% | 44.24% | NA |
| Indica I | 595 | 24.40% | 21.50% | 1.18% | 52.94% | NA |
| Indica II | 465 | 53.50% | 8.80% | 0.22% | 37.42% | NA |
| Indica III | 913 | 52.00% | 1.10% | 0.77% | 46.11% | NA |
| Indica Intermediate | 786 | 49.50% | 7.90% | 2.04% | 40.59% | NA |
| Temperate Japonica | 767 | 0.40% | 96.70% | 0.52% | 2.35% | NA |
| Tropical Japonica | 504 | 1.80% | 7.30% | 20.44% | 70.44% | NA |
| Japonica Intermediate | 241 | 2.50% | 68.90% | 1.66% | 26.97% | NA |
| VI/Aromatic | 96 | 8.30% | 3.10% | 8.33% | 80.21% | NA |
| Intermediate | 90 | 35.60% | 28.90% | 8.89% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409847596 | A -> DEL | N | N | silent_mutation | Average:41.054; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 | N | N | N | N |
| vg0409847596 | A -> G | LOC_Os04g17910.1 | downstream_gene_variant ; 1382.0bp to feature; MODIFIER | silent_mutation | Average:41.054; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 | N | N | N | N |
| vg0409847596 | A -> G | LOC_Os04g17900.1 | intron_variant ; MODIFIER | silent_mutation | Average:41.054; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0409847596 | 2.79E-06 | 2.79E-06 | mr1526 | 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 |
| vg0409847596 | NA | 6.09E-17 | mr1846_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 |
| vg0409847596 | NA | 5.70E-13 | mr1846_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 |