| Variant ID: vg0627586702 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 27586702 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTCAAAACCTCATACTACTTGGGGCTCAATCTTTTAGGGTATTCTGCTTTAATAATAGAGTTCTTGCTAATTATGTCATACCCCTATAGTTGACATCATG[A/T]
CATGGAATGTTCATGGGTTAAATAGACCGGGTAGAAGAGCAACGGTTAGAGAAACGCTGCAAACGGCGAAGCCCCACATCGCCTACCTGCAAGAGACAAA
TTTGTCTCTTGCAGGTAGGCGATGTGGGGCTTCGCCGTTTGCAGCGTTTCTCTAACCGTTGCTCTTCTACCCGGTCTATTTAACCCATGAACATTCCATG[T/A]
CATGATGTCAACTATAGGGGTATGACATAATTAGCAAGAACTCTATTATTAAAGCAGAATACCCTAAAAGATTGAGCCCCAAGTAGTATGAGGTTTTGAC
| 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 | 78.70% | 15.80% | 5.46% | 0.00% | NA |
| All Indica | 2759 | 92.00% | 3.10% | 4.86% | 0.00% | NA |
| All Japonica | 1512 | 49.50% | 43.00% | 7.54% | 0.00% | NA |
| Aus | 269 | 96.30% | 1.10% | 2.60% | 0.00% | NA |
| Indica I | 595 | 80.00% | 7.90% | 12.10% | 0.00% | NA |
| Indica II | 465 | 91.60% | 3.40% | 4.95% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.30% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 92.90% | 2.50% | 4.58% | 0.00% | NA |
| Temperate Japonica | 767 | 16.80% | 74.10% | 9.13% | 0.00% | NA |
| Tropical Japonica | 504 | 87.50% | 8.70% | 3.77% | 0.00% | NA |
| Japonica Intermediate | 241 | 73.90% | 15.80% | 10.37% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 8.90% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0627586702 | A -> T | LOC_Os06g45560.1 | intron_variant ; MODIFIER | silent_mutation | Average:51.894; most accessible tissue: Callus, score: 69.322 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0627586702 | 1.57E-06 | NA | mr1554 | 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 |
| vg0627586702 | 4.33E-06 | 5.73E-07 | mr1554 | Jap_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 |
| vg0627586702 | NA | 1.04E-06 | mr1554_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 |
| vg0627586702 | NA | 4.15E-06 | mr1977_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 |