| Variant ID: vg1101014603 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1014603 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 78. )
ACATAATTGTATCAGTCTCCAGAACTTGCAAGAATCAAACTGATGGAGGAAAAAACCAATGCTCTTGCTTAACTCAAAAAGAGATTAAATTCAATCTGGT[A/T]
AGGAAGGAGGTTTTCTGGACCTCCTATCAATGGCGGAGGGGATCAGCTTGCGACGACGAGCCCGGCGACTCCGGCCGACGGTGATCTGAGGGGCGCACAG
CTGTGCGCCCCTCAGATCACCGTCGGCCGGAGTCGCCGGGCTCGTCGTCGCAAGCTGATCCCCTCCGCCATTGATAGGAGGTCCAGAAAACCTCCTTCCT[T/A]
ACCAGATTGAATTTAATCTCTTTTTGAGTTAAGCAAGAGCATTGGTTTTTTCCTCCATCAGTTTGATTCTTGCAAGTTCTGGAGACTGATACAATTATGT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.80% | 4.40% | 1.80% | 0.00% | NA |
| All Indica | 2759 | 98.90% | 0.80% | 0.25% | 0.00% | NA |
| All Japonica | 1512 | 83.50% | 12.00% | 4.43% | 0.00% | NA |
| Aus | 269 | 97.40% | 0.00% | 2.60% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.10% | 0.43% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.10% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 97.60% | 2.20% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 92.30% | 4.20% | 3.52% | 0.00% | NA |
| Tropical Japonica | 504 | 77.80% | 18.10% | 4.17% | 0.00% | NA |
| Japonica Intermediate | 241 | 67.60% | 24.50% | 7.88% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 5.60% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101014603 | A -> T | LOC_Os11g02930.1 | upstream_gene_variant ; 1683.0bp to feature; MODIFIER | silent_mutation | Average:59.314; most accessible tissue: Zhenshan97 young leaf, score: 74.302 | N | N | N | N |
| vg1101014603 | A -> T | LOC_Os11g02940.1 | upstream_gene_variant ; 2175.0bp to feature; MODIFIER | silent_mutation | Average:59.314; most accessible tissue: Zhenshan97 young leaf, score: 74.302 | N | N | N | N |
| vg1101014603 | A -> T | LOC_Os11g02920.1 | downstream_gene_variant ; 4594.0bp to feature; MODIFIER | silent_mutation | Average:59.314; most accessible tissue: Zhenshan97 young leaf, score: 74.302 | N | N | N | N |
| vg1101014603 | A -> T | LOC_Os11g02930-LOC_Os11g02940 | intergenic_region ; MODIFIER | silent_mutation | Average:59.314; most accessible tissue: Zhenshan97 young leaf, score: 74.302 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1101014603 | 5.89E-06 | NA | mr1082 | 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 |
| vg1101014603 | NA | 2.01E-07 | mr1408 | 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 |
| vg1101014603 | 5.26E-07 | NA | mr1226_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 |
| vg1101014603 | 2.53E-06 | 9.47E-08 | mr1923_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 |