| Variant ID: vg1120087774 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20087774 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 350. )
TCATCAAGACAAACATGGTGCTCAAAGATTTTGGTGGCAATACATCAGAAACTAAAGGGGTTCTGAACGTGGAGCTGACAGTCGGCAGTAAAACCATCCC[T/A]
ACAACATTCTTTGTCATCGATGGGAAGGGTTCTTATAGCTTGTTGCTTGGAAGGGATTGGATTCATGCTAATTGTTGTATTTCTTCAACCATGCACCAAT
ATTGGTGCATGGTTGAAGAAATACAACAATTAGCATGAATCCAATCCCTTCCAAGCAACAAGCTATAAGAACCCTTCCCATCGATGACAAAGAATGTTGT[A/T]
GGGATGGTTTTACTGCCGACTGTCAGCTCCACGTTCAGAACCCCTTTAGTTTCTGATGTATTGCCACCAAAATCTTTGAGCACCATGTTTGTCTTGATGA
| 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 | 92.50% | 6.90% | 0.32% | 0.23% | NA |
| All Indica | 2759 | 88.50% | 10.50% | 0.54% | 0.40% | NA |
| All Japonica | 1512 | 98.60% | 1.40% | 0.00% | 0.00% | 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 | 70.50% | 25.80% | 2.15% | 1.51% | NA |
| Indica III | 913 | 91.90% | 7.70% | 0.33% | 0.11% | NA |
| Indica Intermediate | 786 | 86.60% | 12.70% | 0.25% | 0.38% | NA |
| Temperate Japonica | 767 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 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 | 81.10% | 18.90% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1120087774 | T -> A | LOC_Os11g34290.1 | synonymous_variant ; p.Pro921Pro; LOW | synonymous_codon | Average:49.729; most accessible tissue: Minghui63 young leaf, score: 77.243 | N | N | N | N |
| vg1120087774 | T -> DEL | LOC_Os11g34290.1 | N | frameshift_variant | Average:49.729; most accessible tissue: Minghui63 young leaf, score: 77.243 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1120087774 | 6.23E-06 | NA | mr1770 | 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 |
| vg1120087774 | NA | 3.98E-06 | mr1795_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 |
| vg1120087774 | 4.84E-06 | NA | mr1944_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 |