| Variant ID: vg0323648273 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 23648273 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCTCAATTATATTACGCAGCTTGGCATGTATGTAGTTGAACTTCTCTTCCCTTCCTTCTGGCGGTGGAGCGCGTGGCCCCTTGAATTGATCCTTGTGGTA[T/C]
CGTACACGTGGGTACGGTGCCAGGAAGCCCATCCTACTCGGATATCCGGAGTCAACAAGAAGATATTTTCCTACAAAATAAAGTTATACATGAAAACTAT
ATAGTTTTCATGTATAACTTTATTTTGTAGGAAAATATCTTCTTGTTGACTCCGGATATCCGAGTAGGATGGGCTTCCTGGCACCGTACCCACGTGTACG[A/G]
TACCACAAGGATCAATTCAAGGGGCCACGCGCTCCACCGCCAGAAGGAAGGGAAGAGAAGTTCAACTACATACATGCCAAGCTGCGTAATATAATTGAGA
| 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 | 26.30% | 0.30% | 11.89% | 61.51% | NA |
| All Indica | 2759 | 2.50% | 0.00% | 6.78% | 90.76% | NA |
| All Japonica | 1512 | 69.40% | 0.80% | 15.21% | 14.62% | NA |
| Aus | 269 | 5.20% | 0.00% | 46.84% | 47.96% | NA |
| Indica I | 595 | 2.20% | 0.00% | 6.05% | 91.76% | NA |
| Indica II | 465 | 1.50% | 0.00% | 6.45% | 92.04% | NA |
| Indica III | 913 | 1.90% | 0.00% | 7.56% | 90.58% | NA |
| Indica Intermediate | 786 | 3.90% | 0.00% | 6.62% | 89.44% | NA |
| Temperate Japonica | 767 | 61.50% | 0.40% | 17.86% | 20.21% | NA |
| Tropical Japonica | 504 | 87.10% | 1.00% | 6.55% | 5.36% | NA |
| Japonica Intermediate | 241 | 57.30% | 1.70% | 24.90% | 16.18% | NA |
| VI/Aromatic | 96 | 77.10% | 0.00% | 3.12% | 19.79% | NA |
| Intermediate | 90 | 44.40% | 0.00% | 17.78% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0323648273 | T -> C | LOC_Os03g42510.1 | synonymous_variant ; p.Arg575Arg; LOW | synonymous_codon | Average:6.671; most accessible tissue: Callus, score: 13.771 | N | N | N | N |
| vg0323648273 | T -> DEL | LOC_Os03g42510.1 | N | frameshift_variant | Average:6.671; most accessible tissue: Callus, score: 13.771 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0323648273 | 1.36E-06 | NA | mr1701 | 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 |
| vg0323648273 | NA | 3.67E-06 | mr1051_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 |