| Variant ID: vg1005035532 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 5035532 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.83, G: 0.19, others allele: 0.00, population size: 36. )
CACCAATGATGTAAGCAACACGCAAAACCCACACACGCACAAGCAAACTAACACATCGAACTATGGCAACGGTCTAACTAGGCAACTAATCCCGCCTTGC[A/G]
TCGGAACGAAGAGATGGATCTTCTTCCTCTGGAGTAGCTGGCTCTCTTTCTTCTGGGTCTTCCTCCTCTTCATCATTACTTAAGACATGGATGATAGGTT
AACCTATCATCCATGTCTTAAGTAATGATGAAGAGGAGGAAGACCCAGAAGAAAGAGAGCCAGCTACTCCAGAGGAAGAAGATCCATCTCTTCGTTCCGA[T/C]
GCAAGGCGGGATTAGTTGCCTAGTTAGACCGTTGCCATAGTTCGATGTGTTAGTTTGCTTGTGCGTGTGTGGGTTTTGCGTGTTGCTTACATCATTGGTG
| 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 | 47.90% | 31.20% | 4.87% | 16.04% | NA |
| All Indica | 2759 | 69.00% | 14.30% | 4.06% | 12.69% | NA |
| All Japonica | 1512 | 11.00% | 63.60% | 5.16% | 20.17% | NA |
| Aus | 269 | 60.20% | 12.60% | 10.78% | 16.36% | NA |
| Indica I | 595 | 59.80% | 32.60% | 3.36% | 4.20% | NA |
| Indica II | 465 | 65.40% | 11.80% | 4.09% | 18.71% | NA |
| Indica III | 913 | 71.90% | 2.60% | 4.49% | 21.03% | NA |
| Indica Intermediate | 786 | 74.70% | 15.40% | 4.07% | 5.85% | NA |
| Temperate Japonica | 767 | 4.70% | 76.30% | 1.56% | 17.47% | NA |
| Tropical Japonica | 504 | 18.80% | 48.00% | 11.11% | 22.02% | NA |
| Japonica Intermediate | 241 | 14.90% | 56.00% | 4.15% | 24.90% | NA |
| VI/Aromatic | 96 | 2.10% | 46.90% | 6.25% | 44.79% | NA |
| Intermediate | 90 | 32.20% | 44.40% | 5.56% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1005035532 | A -> G | LOC_Os10g09310.1 | intron_variant ; MODIFIER | silent_mutation | Average:15.757; most accessible tissue: Callus, score: 48.855 | N | N | N | N |
| vg1005035532 | A -> DEL | N | N | silent_mutation | Average:15.757; most accessible tissue: Callus, score: 48.855 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1005035532 | 3.41E-07 | 3.39E-19 | mr1768 | 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 |
| vg1005035532 | 6.40E-08 | 1.82E-29 | mr1768_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 |
| vg1005035532 | NA | 1.60E-08 | mr1768_2 | Ind_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 |
| vg1005035532 | NA | 5.58E-06 | mr1768_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 |