| Variant ID: vg0502367280 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 2367280 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 107. )
TGAACAATATTTTAAATTGTACAAATCATTCATAGCGGATAAATTTACATAAATTTTGATACAAAAATGATTTAGTTTGTACAGTACAAGTTTCAGTTTC[A/G]
TATTTTGATAAGTTTAGTCTAACTTTAGTTTCATATTTTGTATAGTACAAGGACATTTTGCTCCAGTTACTCATAACTCCTTTTAGCAAAATCATGTTGG
CCAACATGATTTTGCTAAAAGGAGTTATGAGTAACTGGAGCAAAATGTCCTTGTACTATACAAAATATGAAACTAAAGTTAGACTAAACTTATCAAAATA[T/C]
GAAACTGAAACTTGTACTGTACAAACTAAATCATTTTTGTATCAAAATTTATGTAAATTTATCCGCTATGAATGATTTGTACAATTTAAAATATTGTTCA
| 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 | 85.40% | 2.50% | 1.27% | 10.88% | NA |
| All Indica | 2759 | 78.10% | 4.20% | 1.99% | 15.69% | NA |
| All Japonica | 1512 | 99.60% | 0.10% | 0.00% | 0.33% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.74% | 0.00% | NA |
| Indica I | 595 | 96.50% | 0.20% | 3.36% | 0.00% | NA |
| Indica II | 465 | 75.70% | 15.70% | 4.09% | 4.52% | NA |
| Indica III | 913 | 61.60% | 0.30% | 0.66% | 37.46% | NA |
| Indica Intermediate | 786 | 85.00% | 4.80% | 1.27% | 8.91% | NA |
| Temperate Japonica | 767 | 99.60% | 0.10% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 28.10% | 0.00% | 2.08% | 69.79% | NA |
| Intermediate | 90 | 87.80% | 1.10% | 1.11% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0502367280 | A -> DEL | N | N | silent_mutation | Average:16.894; most accessible tissue: Callus, score: 75.455 | N | N | N | N |
| vg0502367280 | A -> G | LOC_Os05g04914.1 | intron_variant ; MODIFIER | silent_mutation | Average:16.894; most accessible tissue: Callus, score: 75.455 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0502367280 | NA | 2.76E-06 | mr1818 | 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 |
| vg0502367280 | NA | 1.00E-06 | mr1949 | Ind_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 |
| vg0502367280 | NA | 6.77E-08 | mr1949_2 | Ind_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 |