| Variant ID: vg1105342781 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5342781 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 277. )
AGTTCCCAACTTTTTCTTCAAACTTCCAACTTTTCCATCACATGAAAACTTTCCTACACAAATAAACTTCTAACTTTTTTCTTCAAACTTCCAATTTTAG[T/C]
CAAACTTCCAATTTTAGCGTGGAACTAAACACAGCCCTACTACAAATCCAAAAGTCTGCCCCTTCAAGCTACTTAGAGGGAGAAAAACACCAATGTTACC
GGTAACATTGGTGTTTTTCTCCCTCTAAGTAGCTTGAAGGGGCAGACTTTTGGATTTGTAGTAGGGCTGTGTTTAGTTCCACGCTAAAATTGGAAGTTTG[A/G]
CTAAAATTGGAAGTTTGAAGAAAAAAGTTAGAAGTTTATTTGTGTAGGAAAGTTTTCATGTGATGGAAAAGTTGGAAGTTTGAAGAAAAAGTTGGGAACT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 76.40% | 23.50% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 91.70% | 8.20% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 42.70% | 57.10% | 0.13% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.80% | 3.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 92.90% | 7.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 83.70% | 16.00% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 39.80% | 60.10% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 38.90% | 61.10% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 60.20% | 39.40% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1105342781 | T -> C | LOC_Os11g09970.1 | 3_prime_UTR_variant ; 145.0bp to feature; MODIFIER | silent_mutation | Average:67.149; most accessible tissue: Callus, score: 85.918 | N | N | N | N |
| vg1105342781 | T -> C | LOC_Os11g09960.1 | upstream_gene_variant ; 2276.0bp to feature; MODIFIER | silent_mutation | Average:67.149; most accessible tissue: Callus, score: 85.918 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1105342781 | NA | 9.52E-06 | Awn_length | Ind_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1105342781 | NA | 9.14E-12 | mr1097_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 |
| vg1105342781 | NA | 3.30E-06 | mr1624_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 |
| vg1105342781 | NA | 4.73E-08 | mr1681_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 |
| vg1105342781 | NA | 2.10E-08 | mr1723_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 |