| Variant ID: vg1124566520 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 24566520 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.68, G: 0.31, others allele: 0.00, population size: 72. )
TTTCAGCACTGGTATATATCGTATAGTTCAAGCAGATAACGAGCTTCATCCCCTTCTTTTCCAGTCCACACATTTGCCTGAATGATCTCTTTCAGCAAGA[A/G]
CAATATCTGCTTTTATACCACCTGCTATTGGCATAGAGCGAAAATTTATCGATGCTTTCCAAGGCTATATATATTAAAGTAAAAAGTACGAATTACCCCC
GGGGGTAATTCGTACTTTTTACTTTAATATATATAGCCTTGGAAAGCATCGATAAATTTTCGCTCTATGCCAATAGCAGGTGGTATAAAAGCAGATATTG[T/C]
TCTTGCTGAAAGAGATCATTCAGGCAAATGTGTGGACTGGAAAAGAAGGGGATGAAGCTCGTTATCTGCTTGAACTATACGATATATACCAGTGCTGAAA
| 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 | 33.10% | 22.10% | 0.61% | 44.18% | NA |
| All Indica | 2759 | 42.90% | 3.20% | 0.43% | 53.46% | NA |
| All Japonica | 1512 | 4.80% | 60.90% | 0.73% | 33.60% | NA |
| Aus | 269 | 71.40% | 4.10% | 0.74% | 23.79% | NA |
| Indica I | 595 | 39.50% | 3.70% | 0.34% | 56.47% | NA |
| Indica II | 465 | 63.40% | 5.80% | 0.22% | 30.54% | NA |
| Indica III | 913 | 36.30% | 0.50% | 0.55% | 62.65% | NA |
| Indica Intermediate | 786 | 41.10% | 4.30% | 0.51% | 54.07% | NA |
| Temperate Japonica | 767 | 3.80% | 73.70% | 0.52% | 22.03% | NA |
| Tropical Japonica | 504 | 6.20% | 50.20% | 0.20% | 43.45% | NA |
| Japonica Intermediate | 241 | 5.00% | 42.70% | 2.49% | 49.79% | NA |
| VI/Aromatic | 96 | 81.20% | 1.00% | 3.12% | 14.58% | NA |
| Intermediate | 90 | 44.40% | 24.40% | 1.11% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1124566520 | A -> DEL | N | N | silent_mutation | Average:10.387; most accessible tissue: Callus, score: 60.759 | N | N | N | N |
| vg1124566520 | A -> G | LOC_Os11g41034.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.387; most accessible tissue: Callus, score: 60.759 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1124566520 | NA | 3.33E-10 | mr1191 | 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 |
| vg1124566520 | NA | 8.07E-09 | mr1644 | 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 |
| vg1124566520 | 5.41E-06 | 5.41E-06 | mr1855 | 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 |
| vg1124566520 | 1.36E-06 | 3.77E-17 | mr1416_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 |
| vg1124566520 | NA | 9.80E-08 | mr1662_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 |