| Variant ID: vg1106023109 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 6023109 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 103. )
GAGTAAATACCCCTTAGTGGGTACCAACTATATAGGAAGATACGATTGGGTGGGTTATCTACTTATGCACATCTAACCTACACTAATTGAATAGACAAGT[A/G]
ATCATGAGCTATTAGATTTGCCTCGATCCTATGCGAGATAGAATAAACATGAGCTTAGAGTGGATGTTAAATTTCCTACGTTCTTCCTCTAGAATCATAG
CTATGATTCTAGAGGAAGAACGTAGGAAATTTAACATCCACTCTAAGCTCATGTTTATTCTATCTCGCATAGGATCGAGGCAAATCTAATAGCTCATGAT[T/C]
ACTTGTCTATTCAATTAGTGTAGGTTAGATGTGCATAAGTAGATAACCCACCCAATCGTATCTTCCTATATAGTTGGTACCCACTAAGGGGTATTTACTC
| 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 | 58.90% | 40.80% | 0.32% | 0.00% | NA |
| All Indica | 2759 | 79.60% | 20.10% | 0.33% | 0.00% | NA |
| All Japonica | 1512 | 19.40% | 80.50% | 0.13% | 0.00% | NA |
| Aus | 269 | 90.70% | 7.80% | 1.49% | 0.00% | NA |
| Indica I | 595 | 92.40% | 6.70% | 0.84% | 0.00% | NA |
| Indica II | 465 | 89.20% | 10.50% | 0.22% | 0.00% | NA |
| Indica III | 913 | 70.50% | 29.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 74.60% | 25.10% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 31.20% | 68.60% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 4.00% | 96.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 14.10% | 85.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 11.50% | 88.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 44.40% | 55.60% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1106023109 | A -> G | LOC_Os11g10910.1 | intron_variant ; MODIFIER | silent_mutation | Average:26.254; most accessible tissue: Callus, score: 54.765 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1106023109 | NA | 3.13E-06 | mr1265_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 |
| vg1106023109 | NA | 7.06E-07 | mr1332_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 |
| vg1106023109 | NA | 1.05E-07 | mr1355_2 | 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 |
| vg1106023109 | NA | 7.18E-06 | mr1655_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 |