| Variant ID: vg0220415445 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 20415445 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 313. )
TGAGGCTATAATTGAGCTATGTAGCTTTTTTAGAGAAATTTGTTCCAAGAAATTAGATACTGAAATTCTCAAGAAGCTTGCATCATCAATTGCTGTTACC[C/T]
TCTGTAAGTTAGAGATGATTTTCCCCCCTTCATTCTTTGATGTAATGTTGCATCTACCAATCCATTTAGCCCAGGAAGCTATTACTGGTGGACCTGTCCA
TGGACAGGTCCACCAGTAATAGCTTCCTGGGCTAAATGGATTGGTAGATGCAACATTACATCAAAGAATGAAGGGGGGAAAATCATCTCTAACTTACAGA[G/A]
GGTAACAGCAATTGATGATGCAAGCTTCTTGAGAATTTCAGTATCTAATTTCTTGGAACAAATTTCTCTAAAAAAGCTACATAGCTCAATTATAGCCTCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.50% | 2.10% | 1.02% | 2.33% | NA |
| All Indica | 2759 | 91.20% | 3.10% | 1.74% | 3.99% | NA |
| All Japonica | 1512 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 87.10% | 4.00% | 2.02% | 6.89% | NA |
| Indica II | 465 | 92.00% | 2.60% | 1.29% | 4.09% | NA |
| Indica III | 913 | 97.00% | 1.00% | 0.55% | 1.42% | NA |
| Indica Intermediate | 786 | 86.90% | 5.20% | 3.18% | 4.71% | NA |
| Temperate Japonica | 767 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 7.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0220415445 | C -> T | LOC_Os02g34130.1 | missense_variant ; p.Leu706Phe; MODERATE | nonsynonymous_codon ; L706F | Average:33.371; most accessible tissue: Minghui63 flag leaf, score: 57.881 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0220415445 | C -> DEL | LOC_Os02g34130.1 | N | frameshift_variant | Average:33.371; most accessible tissue: Minghui63 flag leaf, score: 57.881 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0220415445 | 3.54E-06 | NA | mr1770_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 |
| vg0220415445 | 7.09E-07 | NA | mr1946_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 |
| vg0220415445 | 7.09E-07 | NA | mr1948_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 |