| Variant ID: vg0403298006 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 3298006 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGACGAGCGAGGAGACCCCGAGCATGGCGTCGCCGCCATTGCTGATGATGAAGGAGATGTTCTTCAGCAGGAAAGGGAATGGTGACGCCGATCCAAGCAG[C/T]
TGATACCACACGCCAGCCTGCTGCCGCCTCGAGAGAACGGTGTCCTCCAAGGAGTAGGCGGTGAAGTTGTCAGGCATGCCGGCGTGCAGCAGCATGAACG
CGTTCATGCTGCTGCACGCCGGCATGCCTGACAACTTCACCGCCTACTCCTTGGAGGACACCGTTCTCTCGAGGCGGCAGCAGGCTGGCGTGTGGTATCA[G/A]
CTGCTTGGATCGGCGTCACCATTCCCTTTCCTGCTGAAGAACATCTCCTTCATCATCAGCAATGGCGGCGACGCCATGCTCGGGGTCTCCTCGCTCGTCT
| 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 | 45.40% | 11.90% | 1.16% | 41.60% | NA |
| All Indica | 2759 | 20.80% | 11.20% | 1.56% | 66.40% | NA |
| All Japonica | 1512 | 80.30% | 15.80% | 0.60% | 3.31% | NA |
| Aus | 269 | 97.00% | 0.40% | 0.00% | 2.60% | NA |
| Indica I | 595 | 16.00% | 1.30% | 3.53% | 79.16% | NA |
| Indica II | 465 | 27.50% | 3.00% | 1.08% | 68.39% | NA |
| Indica III | 913 | 16.20% | 23.00% | 0.55% | 60.24% | NA |
| Indica Intermediate | 786 | 25.80% | 9.90% | 1.53% | 62.72% | NA |
| Temperate Japonica | 767 | 78.20% | 18.10% | 0.91% | 2.74% | NA |
| Tropical Japonica | 504 | 86.70% | 8.30% | 0.20% | 4.76% | NA |
| Japonica Intermediate | 241 | 73.40% | 24.10% | 0.41% | 2.07% | NA |
| VI/Aromatic | 96 | 58.30% | 1.00% | 1.04% | 39.58% | NA |
| Intermediate | 90 | 43.30% | 11.10% | 2.22% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0403298006 | C -> DEL | LOC_Os04g06300.1 | N | frameshift_variant | Average:36.061; most accessible tissue: Callus, score: 65.689 | N | N | N | N |
| vg0403298006 | C -> T | LOC_Os04g06300.1 | synonymous_variant ; p.Gln119Gln; LOW | synonymous_codon | Average:36.061; most accessible tissue: Callus, score: 65.689 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0403298006 | NA | 9.06E-06 | Yield | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0403298006 | 4.89E-06 | NA | mr1069 | 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 |
| vg0403298006 | NA | 7.43E-06 | mr1149 | 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 |