| Variant ID: vg0810439225 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 10439225 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 313. )
CCTCTTATCCACTCGCAAGCAGTACGGGTGGTAGAACCCTAGCTCTACCGATTCCATCCAAACAGTGCCCATTCCCACCGATTCCGTCACCCTCGATACT[G/A]
GCTGTGCCCAGGCATTGTCGCTGGTGGGATGCAAGTTTGACCGGCGGTGATGGCTTCACCGTCGTAGGAGGCGGTGGAATCTGCGCTGGCGGCAGCGCCG
CGGCGCTGCCGCCAGCGCAGATTCCACCGCCTCCTACGACGGTGAAGCCATCACCGCCGGTCAAACTTGCATCCCACCAGCGACAATGCCTGGGCACAGC[C/T]
AGTATCGAGGGTGACGGAATCGGTGGGAATGGGCACTGTTTGGATGGAATCGGTAGAGCTAGGGTTCTACCACCCGTACTGCTTGCGAGTGGATAAGAGG
| 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 | 95.90% | 3.40% | 0.70% | 0.00% | NA |
| All Indica | 2759 | 98.80% | 1.10% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 89.70% | 8.40% | 1.85% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 96.80% | 3.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.60% | 1.30% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 85.90% | 11.00% | 3.13% | 0.00% | NA |
| Tropical Japonica | 504 | 91.10% | 8.30% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 5.60% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0810439225 | G -> A | LOC_Os08g17050.1 | downstream_gene_variant ; 3701.0bp to feature; MODIFIER | silent_mutation | Average:52.48; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 | N | N | N | N |
| vg0810439225 | G -> A | LOC_Os08g17040.1 | intron_variant ; MODIFIER | silent_mutation | Average:52.48; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0810439225 | 1.56E-08 | NA | mr1002_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 |
| vg0810439225 | NA | 3.82E-06 | mr1062_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 |