| Variant ID: vg0407782850 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 7782850 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GCGTCTGGTCTCCGTGGATTATCCGGATTTCCAGCGTCTGGTGGACAAGAGCATCCGCTTGGAAGCCAAGCACAAGGAACTGGAGTCGCACAAGCGTCGC[T/C]
TGGTGAATTTCCGCAATCAACAGGGGGCTAACCAAAGGGTCTGCTACACCAATCCCTATCCAGGTGGATCCTCCTCGCTGCAGCAGCAGCAACCTCGCTC
GAGCGAGGTTGCTGCTGCTGCAGCGAGGAGGATCCACCTGGATAGGGATTGGTGTAGCAGACCCTTTGGTTAGCCCCCTGTTGATTGCGGAAATTCACCA[A/G]
GCGACGCTTGTGCGACTCCAGTTCCTTGTGCTTGGCTTCCAAGCGGATGCTCTTGTCCACCAGACGCTGGAAATCCGGATAATCCACGGAGACCAGACGC
| 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 | 75.50% | 6.90% | 13.18% | 4.38% | NA |
| All Indica | 2759 | 76.30% | 7.10% | 16.31% | 0.36% | NA |
| All Japonica | 1512 | 81.70% | 0.50% | 5.09% | 12.63% | NA |
| Aus | 269 | 31.20% | 43.50% | 24.16% | 1.12% | NA |
| Indica I | 595 | 63.40% | 7.90% | 28.74% | 0.00% | NA |
| Indica II | 465 | 77.20% | 6.70% | 14.62% | 1.51% | NA |
| Indica III | 913 | 83.20% | 7.30% | 9.20% | 0.22% | NA |
| Indica Intermediate | 786 | 77.40% | 6.40% | 16.16% | 0.13% | NA |
| Temperate Japonica | 767 | 97.70% | 0.00% | 0.26% | 2.09% | NA |
| Tropical Japonica | 504 | 55.40% | 1.40% | 12.70% | 30.56% | NA |
| Japonica Intermediate | 241 | 86.30% | 0.40% | 4.56% | 8.71% | NA |
| VI/Aromatic | 96 | 70.80% | 4.20% | 25.00% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 2.20% | 7.78% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0407782850 | T -> C | LOC_Os04g13930.1 | synonymous_variant ; p.Leu480Leu; LOW | synonymous_codon | Average:13.23; most accessible tissue: Callus, score: 30.616 | N | N | N | N |
| vg0407782850 | T -> DEL | LOC_Os04g13930.1 | N | frameshift_variant | Average:13.23; most accessible tissue: Callus, score: 30.616 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0407782850 | NA | 1.06E-09 | mr1118 | 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 |
| vg0407782850 | NA | 4.48E-06 | mr1496 | 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 |
| vg0407782850 | 1.66E-06 | 4.51E-15 | mr1118_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 |
| vg0407782850 | NA | 7.55E-07 | mr1496_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 |