| Variant ID: vg1118805754 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 18805754 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.53, T: 0.45, others allele: 0.00, population size: 159. )
TTGATTCAAACACGTCTTAATGGTTTTTCTAATTTGTAGCATACCTAAAATAATTTACATACAGATATTTTTTTCTACTTTTTCTCACTAGTTCCCCTGA[C/T]
ATTTTATCCCCCTACAACCTAACACAATGACAAGAACAACAGTTCCACGAAAGCCTATATTTCAGTGCATCCTGTATATGTTGGGCTCCATGCACATGCA
TGCATGTGCATGGAGCCCAACATATACAGGATGCACTGAAATATAGGCTTTCGTGGAACTGTTGTTCTTGTCATTGTGTTAGGTTGTAGGGGGATAAAAT[G/A]
TCAGGGGAACTAGTGAGAAAAAGTAGAAAAAAATATCTGTATGTAAATTATTTTAGGTATGCTACAAATTAGAAAAACCATTAAGACGTGTTTGAATCAA
| 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 | 52.00% | 47.90% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 73.60% | 26.30% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 4.40% | 95.60% | 0.00% | 0.00% | NA |
| Aus | 269 | 95.20% | 4.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 88.60% | 11.40% | 0.00% | 0.00% | NA |
| Indica II | 465 | 68.00% | 32.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 70.20% | 29.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 69.70% | 30.20% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 4.00% | 96.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 5.80% | 94.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.90% | 97.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 59.40% | 39.60% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 50.00% | 46.70% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1118805754 | C -> T | LOC_Os11g31970.1 | upstream_gene_variant ; 4575.0bp to feature; MODIFIER | silent_mutation | Average:63.403; most accessible tissue: Zhenshan97 panicle, score: 83.41 | N | N | N | N |
| vg1118805754 | C -> T | LOC_Os11g31970-LOC_Os11g31980 | intergenic_region ; MODIFIER | silent_mutation | Average:63.403; most accessible tissue: Zhenshan97 panicle, score: 83.41 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1118805754 | NA | 5.81E-07 | mr1044 | 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 |
| vg1118805754 | NA | 3.81E-06 | mr1633 | 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 |
| vg1118805754 | NA | 7.89E-07 | mr1790 | Ind_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 |