| Variant ID: vg1006706089 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 6706089 |
| 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: 70. )
GTTTAGTCTATGGTTGATTTGCATGGTTCAACCTCAATGCTAACCCTGTGTGCTTGCTGAAATCCCTCCAACTCTATAACAGGAGGTCTCATGGGGATCA[A/G]
TGGCGAGGTGGTTTTCAGCCAACACAGCTCTGCATCGAGCTTGCGTCCTCAGGTCCATCTTTTCAATCTCATCTCACTTAGATAGCGACCAGATGGTTGG
CCAACCATCTGGTCGCTATCTAAGTGAGATGAGATTGAAAAGATGGACCTGAGGACGCAAGCTCGATGCAGAGCTGTGTTGGCTGAAAACCACCTCGCCA[T/C]
TGATCCCCATGAGACCTCCTGTTATAGAGTTGGAGGGATTTCAGCAAGCACACAGGGTTAGCATTGAGGTTGAACCATGCAAATCAACCATAGACTAAAC
| 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 | 37.70% | 4.40% | 3.55% | 54.32% | NA |
| All Indica | 2759 | 36.00% | 4.30% | 3.81% | 55.96% | NA |
| All Japonica | 1512 | 48.70% | 0.50% | 3.24% | 47.55% | NA |
| Aus | 269 | 3.00% | 1.50% | 3.35% | 92.19% | NA |
| Indica I | 595 | 12.60% | 1.30% | 4.87% | 81.18% | NA |
| Indica II | 465 | 60.60% | 1.10% | 3.23% | 35.05% | NA |
| Indica III | 913 | 32.10% | 8.40% | 2.96% | 56.52% | NA |
| Indica Intermediate | 786 | 43.50% | 3.60% | 4.33% | 48.60% | NA |
| Temperate Japonica | 767 | 71.40% | 0.00% | 2.61% | 25.95% | NA |
| Tropical Japonica | 504 | 11.10% | 0.40% | 4.76% | 83.73% | NA |
| Japonica Intermediate | 241 | 55.20% | 2.10% | 2.07% | 40.66% | NA |
| VI/Aromatic | 96 | 7.30% | 69.80% | 1.04% | 21.88% | NA |
| Intermediate | 90 | 44.40% | 12.20% | 4.44% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1006706089 | A -> G | LOC_Os10g12050.1 | downstream_gene_variant ; 3604.0bp to feature; MODIFIER | silent_mutation | Average:11.336; most accessible tissue: Callus, score: 57.752 | N | N | N | N |
| vg1006706089 | A -> G | LOC_Os10g12050.2 | downstream_gene_variant ; 3714.0bp to feature; MODIFIER | silent_mutation | Average:11.336; most accessible tissue: Callus, score: 57.752 | N | N | N | N |
| vg1006706089 | A -> G | LOC_Os10g12050-LOC_Os10g12080 | intergenic_region ; MODIFIER | silent_mutation | Average:11.336; most accessible tissue: Callus, score: 57.752 | N | N | N | N |
| vg1006706089 | A -> DEL | N | N | silent_mutation | Average:11.336; most accessible tissue: Callus, score: 57.752 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1006706089 | NA | 5.85E-08 | mr1136 | 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 |
| vg1006706089 | NA | 3.62E-06 | mr1448 | 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 |
| vg1006706089 | NA | 1.99E-10 | mr1570 | 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 |
| vg1006706089 | NA | 3.46E-06 | mr1596 | 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 |
| vg1006706089 | 1.60E-06 | NA | mr1949 | 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 |
| vg1006706089 | NA | 5.31E-06 | mr1850_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 |