| Variant ID: vg0212281281 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 12281281 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGCCAGGACAACAATGGTGGACGACGATAGAATTCCCGAGAACCTGAACATCGCCCTCGGAATCGGACACCGGAGCCGGGTGACCCATCGTCATCGTAGT[C/T]
TTCATCTTCATCCTCGTCATCCGATAGACATCCACGGAGGACACACGATCGCCGACAACCCACCGCCCCCAGCGCCGGGTGTAGAGCTTTCAACAATTCT
AGAATTGTTGAAAGCTCTACACCCGGCGCTGGGGGCGGTGGGTTGTCGGCGATCGTGTGTCCTCCGTGGATGTCTATCGGATGACGAGGATGAAGATGAA[G/A]
ACTACGATGACGATGGGTCACCCGGCTCCGGTGTCCGATTCCGAGGGCGATGTTCAGGTTCTCGGGAATTCTATCGTCGTCCACCATTGTTGTCCTGGCG
| 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 | 92.90% | 6.60% | 0.42% | 0.00% | NA |
| All Indica | 2759 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 86.80% | 12.00% | 1.19% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.30% | 2.70% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 97.80% | 1.20% | 1.04% | 0.00% | NA |
| Tropical Japonica | 504 | 82.90% | 16.70% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 60.20% | 36.50% | 3.32% | 0.00% | NA |
| VI/Aromatic | 96 | 4.20% | 93.80% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 14.40% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0212281281 | C -> T | LOC_Os02g20800.1 | intron_variant ; MODIFIER | silent_mutation | Average:59.559; most accessible tissue: Minghui63 young leaf, score: 75.937 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0212281281 | NA | 6.75E-06 | mr1695 | 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 |
| vg0212281281 | 1.44E-06 | NA | mr1350_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 |