| Variant ID: vg0221725390 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21725390 |
| Reference Allele: C | Alternative Allele: T,A |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GGTGGGAGAACTACTGCAATACACACCCTGAACTCACTAACATTACTTGGGATGAGTTTGCTACGGCTTTCCGTGCAGCTCATGTGCCTGAAAGCACCAT[C/T,A]
GATATGAAGAAAGAGGAATTTAACAGGCTTAAGCAAGGCAACAACAGTGTCAATGAGTACCTAAGTCAGTTCAACAAGTTGGCTCGGTACGCCCCTGAGG
CCTCAGGGGCGTACCGAGCCAACTTGTTGAACTGACTTAGGTACTCATTGACACTGTTGTTGCCTTGCTTAAGCCTGTTAAATTCCTCTTTCTTCATATC[G/A,T]
ATGGTGCTTTCAGGCACATGAGCTGCACGGAAAGCCGTAGCAAACTCATCCCAAGTAATGTTAGTGAGTTCAGGGTGTGTATTGCAGTAGTTCTCCCACC
| 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 | 63.80% | 28.30% | 5.29% | 2.45% | A: 0.15% |
| All Indica | 2759 | 94.90% | 2.70% | 2.07% | 0.11% | A: 0.25% |
| All Japonica | 1512 | 8.20% | 74.50% | 9.85% | 7.41% | NA |
| Aus | 269 | 84.40% | 2.20% | 13.38% | 0.00% | NA |
| Indica I | 595 | 97.30% | 1.70% | 0.67% | 0.34% | NA |
| Indica II | 465 | 89.50% | 1.90% | 7.96% | 0.00% | A: 0.65% |
| Indica III | 913 | 97.50% | 2.00% | 0.33% | 0.00% | A: 0.22% |
| Indica Intermediate | 786 | 93.30% | 4.70% | 1.65% | 0.13% | A: 0.25% |
| Temperate Japonica | 767 | 5.60% | 72.80% | 10.95% | 10.69% | NA |
| Tropical Japonica | 504 | 11.90% | 76.80% | 8.33% | 2.98% | NA |
| Japonica Intermediate | 241 | 8.70% | 75.50% | 9.54% | 6.22% | NA |
| VI/Aromatic | 96 | 9.40% | 88.50% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 42.20% | 50.00% | 6.67% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221725390 | C -> A | LOC_Os02g36100.1 | synonymous_variant ; p.Ile353Ile; LOW | synonymous_codon | Average:12.674; most accessible tissue: Callus, score: 21.416 | N | N | N | N |
| vg0221725390 | C -> T | LOC_Os02g36100.1 | synonymous_variant ; p.Ile353Ile; LOW | synonymous_codon | Average:12.674; most accessible tissue: Callus, score: 21.416 | N | N | N | N |
| vg0221725390 | C -> DEL | LOC_Os02g36100.1 | N | frameshift_variant | Average:12.674; most accessible tissue: Callus, score: 21.416 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0221725390 | NA | 1.84E-10 | mr1128 | 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 |
| vg0221725390 | NA | 1.13E-09 | mr1714 | 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 |
| vg0221725390 | 3.97E-08 | NA | mr1563_2 | 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 |
| vg0221725390 | 3.46E-06 | NA | mr1563_2 | 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 |
| vg0221725390 | NA | 1.11E-08 | mr1600_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 |
| vg0221725390 | NA | 1.21E-07 | mr1783_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 |