| Variant ID: vg0515524688 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 15524688 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GAGCCAGATTCCGATCAAAGTAGAGATCATCAAACTGCTGGAGTTGTAGCTGCTGCGCTATGACCTGAAAAATGTTAATATCCTCATAGTGAGACTGTTG[C/T]
GCCACCAGCCAAAGCTGTTGCCAGACTTGGTTGTTTCTCAGTTGAAACGCAACTGATTGCAATAAGGGGCTTGCCGTTATGCCATACTGCTGCCTTACGA
TCGTAAGGCAGCAGTATGGCATAACGGCAAGCCCCTTATTGCAATCAGTTGCGTTTCAACTGAGAAACAACCAAGTCTGGCAACAGCTTTGGCTGGTGGC[G/A]
CAACAGTCTCACTATGAGGATATTAACATTTTTCAGGTCATAGCGCAGCAGCTACAACTCCAGCAGTTTGATGATCTCTACTTTGATCGGAATCTGGCTC
| 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 | 56.00% | 0.40% | 4.59% | 38.95% | NA |
| All Indica | 2759 | 42.80% | 0.60% | 5.04% | 51.54% | NA |
| All Japonica | 1512 | 78.00% | 0.30% | 0.33% | 21.43% | NA |
| Aus | 269 | 47.60% | 0.00% | 26.02% | 26.39% | NA |
| Indica I | 595 | 26.20% | 0.50% | 1.18% | 72.10% | NA |
| Indica II | 465 | 63.20% | 0.20% | 0.65% | 35.91% | NA |
| Indica III | 913 | 48.70% | 0.90% | 9.53% | 40.85% | NA |
| Indica Intermediate | 786 | 36.40% | 0.60% | 5.34% | 57.63% | NA |
| Temperate Japonica | 767 | 94.30% | 0.10% | 0.13% | 5.48% | NA |
| Tropical Japonica | 504 | 52.00% | 0.60% | 0.79% | 46.63% | NA |
| Japonica Intermediate | 241 | 80.50% | 0.00% | 0.00% | 19.50% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 70.00% | 0.00% | 3.33% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0515524688 | C -> T | LOC_Os05g26750.1 | synonymous_variant ; p.Ala83Ala; LOW | synonymous_codon | Average:21.526; most accessible tissue: Callus, score: 39.575 | N | N | N | N |
| vg0515524688 | C -> DEL | LOC_Os05g26750.1 | N | frameshift_variant | Average:21.526; most accessible tissue: Callus, score: 39.575 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0515524688 | 5.88E-07 | 5.88E-07 | mr1184 | 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 |
| vg0515524688 | NA | 1.29E-07 | mr1243 | 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 |
| vg0515524688 | NA | 4.11E-06 | mr1378 | 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 |
| vg0515524688 | NA | 6.02E-08 | mr1423 | 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 |
| vg0515524688 | NA | 4.42E-07 | mr1951 | 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 |