| Variant ID: vg0911590178 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 11590178 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TACTTTCTTTTAGGTTTGCTTCGAAATAAACATATTCAATATAACTATAATTGTAATTGTAATGTTTCTGAAAAAAATGAGCACTAAAAATGAACTTATT[C/T]
TCTTTTTTTTGGCCCGAGGGACCTAAAATAGACTTATTTCCAACCAATGCCGGTCGGCCCACGGCCTTTTGCACACGCGCGGGCACACTTTTCCTCCCCA
TGGGGAGGAAAAGTGTGCCCGCGCGTGTGCAAAAGGCCGTGGGCCGACCGGCATTGGTTGGAAATAAGTCTATTTTAGGTCCCTCGGGCCAAAAAAAAGA[G/A]
AATAAGTTCATTTTTAGTGCTCATTTTTTTCAGAAACATTACAATTACAATTATAGTTATATTGAATATGTTTATTTCGAAGCAAACCTAAAAGAAAGTA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 70.10% | 3.80% | 9.67% | 16.42% | NA |
| All Indica | 2759 | 64.50% | 5.40% | 13.19% | 16.89% | NA |
| All Japonica | 1512 | 86.80% | 0.10% | 1.32% | 11.84% | NA |
| Aus | 269 | 26.40% | 8.90% | 21.19% | 43.49% | NA |
| Indica I | 595 | 88.60% | 1.20% | 5.88% | 4.37% | NA |
| Indica II | 465 | 71.20% | 0.60% | 10.97% | 17.20% | NA |
| Indica III | 913 | 45.80% | 10.80% | 18.29% | 25.08% | NA |
| Indica Intermediate | 786 | 64.10% | 5.10% | 14.12% | 16.67% | NA |
| Temperate Japonica | 767 | 81.20% | 0.00% | 0.91% | 17.86% | NA |
| Tropical Japonica | 504 | 92.70% | 0.00% | 1.79% | 5.56% | NA |
| Japonica Intermediate | 241 | 92.10% | 0.40% | 1.66% | 5.81% | NA |
| VI/Aromatic | 96 | 85.40% | 2.10% | 8.33% | 4.17% | NA |
| Intermediate | 90 | 76.70% | 3.30% | 8.89% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0911590178 | C -> DEL | N | N | silent_mutation | Average:27.511; most accessible tissue: Zhenshan97 root, score: 58.674 | N | N | N | N |
| vg0911590178 | C -> T | LOC_Os09g19360.1 | upstream_gene_variant ; 1249.0bp to feature; MODIFIER | silent_mutation | Average:27.511; most accessible tissue: Zhenshan97 root, score: 58.674 | N | N | N | N |
| vg0911590178 | C -> T | LOC_Os09g19360-LOC_Os09g19370 | intergenic_region ; MODIFIER | silent_mutation | Average:27.511; most accessible tissue: Zhenshan97 root, score: 58.674 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0911590178 | NA | 1.40E-06 | mr1219_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 |
| vg0911590178 | NA | 4.22E-06 | mr1331_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 |
| vg0911590178 | NA | 5.64E-06 | mr1510_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 |
| vg0911590178 | 1.15E-06 | 3.00E-07 | mr1923_2 | 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 |