| Variant ID: vg1214799098 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 14799098 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 105. )
CATCGGAGATTATCTTGATGAGGCAGAAGAGGATATTTCAAGCAAAGCTCTAGCCCCCTTATCTGACGATGTGAAGAAAACAGTTGAAGATATCTCCCGT[T/C]
GGCTAGAGGCCTCTTCTTTAGATAGCTTGGTGGTCGACTGTGGATCGATTAGGACACGACTACATGAAGTTCAAGCTCTGATTCCCGAAGAACTAGCCGA
TCGGCTAGTTCTTCGGGAATCAGAGCTTGAACTTCATGTAGTCGTGTCCTAATCGATCCACAGTCGACCACCAAGCTATCTAAAGAAGAGGCCTCTAGCC[A/G]
ACGGGAGATATCTTCAACTGTTTTCTTCACATCGTCAGATAAGGGGGCTAGAGCTTTGCTTGAAATATCCTCTTCTGCCTCATCAAGATAATCTCCGATG
| 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 | 38.70% | 32.30% | 17.65% | 11.36% | NA |
| All Indica | 2759 | 56.40% | 15.70% | 23.81% | 4.02% | NA |
| All Japonica | 1512 | 2.00% | 68.10% | 3.24% | 26.72% | NA |
| Aus | 269 | 73.20% | 8.90% | 15.99% | 1.86% | NA |
| Indica I | 595 | 60.70% | 14.50% | 23.19% | 1.68% | NA |
| Indica II | 465 | 54.80% | 11.40% | 26.88% | 6.88% | NA |
| Indica III | 913 | 54.90% | 17.70% | 23.33% | 4.05% | NA |
| Indica Intermediate | 786 | 56.00% | 16.90% | 23.03% | 4.07% | NA |
| Temperate Japonica | 767 | 0.90% | 89.00% | 2.09% | 7.95% | NA |
| Tropical Japonica | 504 | 3.60% | 41.30% | 2.78% | 52.38% | NA |
| Japonica Intermediate | 241 | 2.10% | 57.30% | 7.88% | 32.78% | NA |
| VI/Aromatic | 96 | 15.60% | 5.20% | 66.67% | 12.50% | NA |
| Intermediate | 90 | 33.30% | 37.80% | 23.33% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1214799098 | T -> C | LOC_Os12g25570.1 | missense_variant ; p.Trp566Arg; MODERATE | nonsynonymous_codon ; W566R | Average:15.196; most accessible tissue: Callus, score: 22.083 | unknown | unknown | TOLERATED | 1.00 |
| vg1214799098 | T -> DEL | LOC_Os12g25570.1 | N | frameshift_variant | Average:15.196; most accessible tissue: Callus, score: 22.083 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1214799098 | 2.69E-06 | 1.82E-06 | mr1484 | 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 |
| vg1214799098 | 2.95E-06 | 8.02E-07 | mr1549 | 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 |
| vg1214799098 | 2.17E-06 | 2.17E-06 | mr1572 | 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 |
| vg1214799098 | NA | 2.54E-12 | mr1258_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 |