| Variant ID: vg0314125201 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 14125201 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.69, T: 0.32, others allele: 0.00, population size: 82. )
CACCCGCCACAACCGAGCCACCCAAGAAAATGAGCAAGACAAACAAGACGCCGAAACCGGATGGCGCAATCAAGACCGTTCCTCTCTCTAGTGCCAACCC[T/C]
GACAAGACCGTCAAGATCGGGGCATCACTAAACGAGAAATAGGAACTCGCGCTCATCACCTTCCTCCGCGACAATGCTGACGCGTTCGCTTGGCAGCCGT
ACGGCTGCCAAGCGAACGCGTCAGCATTGTCGCGGAGGAAGGTGATGAGCGCGAGTTCCTATTTCTCGTTTAGTGATGCCCCGATCTTGACGGTCTTGTC[A/G]
GGGTTGGCACTAGAGAGAGGAACGGTCTTGATTGCGCCATCCGGTTTCGGCGTCTTGTTTGTCTTGCTCATTTTCTTGGGTGGCTCGGTTGTGGCGGGTG
| 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 | 44.90% | 33.70% | 10.75% | 10.69% | NA |
| All Indica | 2759 | 70.60% | 3.90% | 10.08% | 15.44% | NA |
| All Japonica | 1512 | 1.10% | 87.80% | 6.75% | 4.37% | NA |
| Aus | 269 | 40.10% | 16.70% | 43.12% | 0.00% | NA |
| Indica I | 595 | 37.50% | 6.40% | 16.97% | 39.16% | NA |
| Indica II | 465 | 64.90% | 4.10% | 12.47% | 18.49% | NA |
| Indica III | 913 | 95.90% | 1.30% | 1.97% | 0.77% | NA |
| Indica Intermediate | 786 | 69.60% | 4.80% | 12.85% | 12.72% | NA |
| Temperate Japonica | 767 | 0.80% | 87.40% | 9.26% | 2.61% | NA |
| Tropical Japonica | 504 | 1.40% | 85.10% | 5.16% | 8.33% | NA |
| Japonica Intermediate | 241 | 1.20% | 95.00% | 2.07% | 1.66% | NA |
| VI/Aromatic | 96 | 15.60% | 75.00% | 5.21% | 4.17% | NA |
| Intermediate | 90 | 37.80% | 44.40% | 7.78% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0314125201 | T -> C | LOC_Os03g24780.1 | synonymous_variant ; p.Pro442Pro; LOW | synonymous_codon | Average:13.279; most accessible tissue: Callus, score: 34.891 | N | N | N | N |
| vg0314125201 | T -> C | LOC_Os03g24780.1 | synonymous_variant ; p.Pro442Pro; LOW | nonsynonymous_codon ; P442L | Average:13.279; most accessible tissue: Callus, score: 34.891 | unknown | unknown | DELETERIOUS | 0.04 |
| vg0314125201 | T -> DEL | LOC_Os03g24780.1 | N | frameshift_variant | Average:13.279; most accessible tissue: Callus, score: 34.891 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0314125201 | NA | 1.03E-11 | mr1322 | 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 |
| vg0314125201 | 7.37E-06 | 6.28E-10 | mr1527 | 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 |
| vg0314125201 | NA | 5.08E-08 | mr1532 | 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 |
| vg0314125201 | NA | 1.51E-06 | mr1728 | 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 |
| vg0314125201 | NA | 1.82E-12 | mr1744 | 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 |