| Variant ID: vg0620149548 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20149548 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, A: 0.03, others allele: 0.00, population size: 213. )
ACACATCATTCAATCCTTCATGGTCACTACTACCAGATTTGTTATCAATGTCGCAGCATGTTTGCTAGTCTATGGCAAGAGAGCCATTCGTATTACTGCC[T/A]
GAGAAAAGCTCTTCATCTCATGAAAGTACTTGATTGGCTTAGCAAGCAAACGCCTATCCCTATCCTGCATGTTGGTACAACAATATAATTTAGTAAAAAA
TTTTTTACTAAATTATATTGTTGTACCAACATGCAGGATAGGGATAGGCGTTTGCTTGCTAAGCCAATCAAGTACTTTCATGAGATGAAGAGCTTTTCTC[A/T]
GGCAGTAATACGAATGGCTCTCTTGCCATAGACTAGCAAACATGCTGCGACATTGATAACAAATCTGGTAGTAGTGACCATGAAGGATTGAATGATGTGT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.70% | 4.00% | 1.08% | 2.29% | NA |
| All Indica | 2759 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 78.00% | 11.60% | 3.37% | 7.01% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 87.90% | 9.80% | 1.30% | 1.04% | NA |
| Tropical Japonica | 504 | 76.80% | 8.10% | 4.17% | 10.91% | NA |
| Japonica Intermediate | 241 | 49.40% | 24.50% | 8.30% | 17.84% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 4.40% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620149548 | T -> A | LOC_Os06g34670.1 | missense_variant ; p.Gln94Leu; MODERATE | nonsynonymous_codon ; Q94L | Average:46.985; most accessible tissue: Callus, score: 68.191 | unknown | unknown | TOLERATED | 0.05 |
| vg0620149548 | T -> DEL | LOC_Os06g34670.1 | N | frameshift_variant | Average:46.985; most accessible tissue: Callus, score: 68.191 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0620149548 | 5.99E-07 | NA | mr1103 | 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 |
| vg0620149548 | 1.20E-06 | NA | mr1103_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 |
| vg0620149548 | 8.80E-06 | NA | mr1104_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 |