| Variant ID: vg0901039207 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 1039207 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AAATCGCCCCCTACAGCCTCCCACCAAAATAGTGAATAGTGGGATACAATTACACTAGGTGGTGGGGGGTATTTATACTGTGCAACAAATATCTGTAACG[G/A]
CCCTAAAACAATCAACCGTGACGGGCATACAAGTAATCTCTATCGGGCCTTAATAAAAGGCCGTAAAAAAAAGTGTCATCTGTGACGGGCACTAAACTTA
TAAGTTTAGTGCCCGTCACAGATGACACTTTTTTTTACGGCCTTTTATTAAGGCCCGATAGAGATTACTTGTATGCCCGTCACGGTTGATTGTTTTAGGG[C/T]
CGTTACAGATATTTGTTGCACAGTATAAATACCCCCCACCACCTAGTGTAATTGTATCCCACTATTCACTATTTTGGTGGGAGGCTGTAGGGGGCGATTT
| 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 | 88.70% | 7.70% | 3.66% | 0.00% | NA |
| All Indica | 2759 | 84.30% | 11.10% | 4.60% | 0.00% | NA |
| All Japonica | 1512 | 96.30% | 1.20% | 2.51% | 0.00% | NA |
| Aus | 269 | 85.50% | 12.60% | 1.86% | 0.00% | NA |
| Indica I | 595 | 71.30% | 19.50% | 9.24% | 0.00% | NA |
| Indica II | 465 | 92.30% | 5.80% | 1.94% | 0.00% | NA |
| Indica III | 913 | 93.10% | 5.70% | 1.20% | 0.00% | NA |
| Indica Intermediate | 786 | 79.10% | 14.20% | 6.62% | 0.00% | NA |
| Temperate Japonica | 767 | 96.30% | 0.50% | 3.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 88.80% | 5.80% | 5.39% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 1.10% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0901039207 | G -> A | LOC_Os09g02500.1 | upstream_gene_variant ; 265.0bp to feature; MODIFIER | silent_mutation | Average:34.281; most accessible tissue: Zhenshan97 flag leaf, score: 70.837 | N | N | N | N |
| vg0901039207 | G -> A | LOC_Os09g02500-LOC_Os09g02510 | intergenic_region ; MODIFIER | silent_mutation | Average:34.281; most accessible tissue: Zhenshan97 flag leaf, score: 70.837 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0901039207 | 2.63E-06 | 2.63E-06 | mr1389 | 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 |
| vg0901039207 | 1.14E-08 | 1.12E-07 | mr1038_2 | 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 |
| vg0901039207 | 2.87E-09 | 2.87E-09 | mr1389_2 | 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 |