| Variant ID: vg1126919326 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26919326 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 35. )
GAATTTGACCTAGAGTTTCACAGGAATTTGAAAGGAAATTCTAATATAGGATTTGAGATCCTTTTGGCACAAAATCAACTAAGAACCAAATTAACTCCAA[T/A]
TTTTAAATGACAAACTTTTTTAAATAAAAGCACATAAAATACGGGTGCTACAGTTGACGACGCAGGGGAGGAGGAGGAGGAGGACGGAGATTCCTGTCGC
GCGACAGGAATCTCCGTCCTCCTCCTCCTCCTCCCCTGCGTCGTCAACTGTAGCACCCGTATTTTATGTGCTTTTATTTAAAAAAGTTTGTCATTTAAAA[A/T]
TTGGAGTTAATTTGGTTCTTAGTTGATTTTGTGCCAAAAGGATCTCAAATCCTATATTAGAATTTCCTTTCAAATTCCTGTGAAACTCTAGGTCAAATTC
| 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 | 45.20% | 3.40% | 26.62% | 24.76% | NA |
| All Indica | 2759 | 49.90% | 3.30% | 35.77% | 10.95% | NA |
| All Japonica | 1512 | 39.40% | 3.80% | 9.33% | 47.49% | NA |
| Aus | 269 | 45.70% | 1.10% | 32.71% | 20.45% | NA |
| Indica I | 595 | 38.80% | 3.00% | 44.71% | 13.45% | NA |
| Indica II | 465 | 35.50% | 4.70% | 36.99% | 22.80% | NA |
| Indica III | 913 | 61.70% | 3.10% | 31.98% | 3.29% | NA |
| Indica Intermediate | 786 | 53.30% | 3.10% | 32.70% | 10.94% | NA |
| Temperate Japonica | 767 | 65.80% | 0.40% | 6.26% | 27.51% | NA |
| Tropical Japonica | 504 | 6.90% | 9.90% | 12.30% | 70.83% | NA |
| Japonica Intermediate | 241 | 22.80% | 2.10% | 12.86% | 62.24% | NA |
| VI/Aromatic | 96 | 12.50% | 2.10% | 13.54% | 71.88% | NA |
| Intermediate | 90 | 33.30% | 5.60% | 32.22% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126919326 | T -> A | LOC_Os11g44510.1 | upstream_gene_variant ; 2091.0bp to feature; MODIFIER | silent_mutation | Average:57.291; most accessible tissue: Zhenshan97 root, score: 89.721 | N | N | N | N |
| vg1126919326 | T -> A | LOC_Os11g44520.1 | upstream_gene_variant ; 4390.0bp to feature; MODIFIER | silent_mutation | Average:57.291; most accessible tissue: Zhenshan97 root, score: 89.721 | N | N | N | N |
| vg1126919326 | T -> A | LOC_Os11g44490.1 | downstream_gene_variant ; 4443.0bp to feature; MODIFIER | silent_mutation | Average:57.291; most accessible tissue: Zhenshan97 root, score: 89.721 | N | N | N | N |
| vg1126919326 | T -> A | LOC_Os11g44500.1 | downstream_gene_variant ; 939.0bp to feature; MODIFIER | silent_mutation | Average:57.291; most accessible tissue: Zhenshan97 root, score: 89.721 | N | N | N | N |
| vg1126919326 | T -> A | LOC_Os11g44500-LOC_Os11g44510 | intergenic_region ; MODIFIER | silent_mutation | Average:57.291; most accessible tissue: Zhenshan97 root, score: 89.721 | N | N | N | N |
| vg1126919326 | T -> DEL | N | N | silent_mutation | Average:57.291; most accessible tissue: Zhenshan97 root, score: 89.721 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1126919326 | NA | 3.22E-06 | mr1548 | Jap_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 |
| vg1126919326 | 3.99E-06 | 6.31E-06 | mr1928 | 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 |
| vg1126919326 | NA | 5.04E-09 | mr1010_2 | Jap_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 |