| Variant ID: vg1221867400 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 21867400 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CAACAGTGTTTAGTTGTCATTCTGAAAAGAAAAAACAATCTAGTGGTATTATGGTACAACTATGTCTATGAAAAGCTGAAAGACGGCAACGGCATATATC[G/A]
TCGCCGGCAGAGTGAGCTAGCAGTACATTTTATTGTGAACATTAGTACAGCTGCAGATGGATCCAAGCTAGCTATCTGTGGTTTAGAAGCGCTTATTCCA
TGGAATAAGCGCTTCTAAACCACAGATAGCTAGCTTGGATCCATCTGCAGCTGTACTAATGTTCACAATAAAATGTACTGCTAGCTCACTCTGCCGGCGA[C/T]
GATATATGCCGTTGCCGTCTTTCAGCTTTTCATAGACATAGTTGTACCATAATACCACTAGATTGTTTTTTCTTTTCAGAATGACAACTAAACACTGTTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.90% | 4.30% | 0.44% | 9.39% | NA |
| All Indica | 2759 | 81.60% | 1.80% | 0.76% | 15.77% | NA |
| All Japonica | 1512 | 95.40% | 4.50% | 0.00% | 0.13% | NA |
| Aus | 269 | 72.90% | 27.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 58.70% | 0.00% | 0.65% | 40.65% | NA |
| Indica III | 913 | 82.80% | 3.50% | 1.64% | 12.05% | NA |
| Indica Intermediate | 786 | 79.90% | 2.40% | 0.38% | 17.30% | NA |
| Temperate Japonica | 767 | 97.30% | 2.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 91.50% | 8.30% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 97.50% | 2.10% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 94.80% | 4.20% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 87.80% | 5.60% | 0.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1221867400 | G -> DEL | N | N | silent_mutation | Average:26.225; most accessible tissue: Callus, score: 57.635 | N | N | N | N |
| vg1221867400 | G -> A | LOC_Os12g35890.1 | upstream_gene_variant ; 2371.0bp to feature; MODIFIER | silent_mutation | Average:26.225; most accessible tissue: Callus, score: 57.635 | N | N | N | N |
| vg1221867400 | G -> A | LOC_Os12g35880.1 | downstream_gene_variant ; 2520.0bp to feature; MODIFIER | silent_mutation | Average:26.225; most accessible tissue: Callus, score: 57.635 | N | N | N | N |
| vg1221867400 | G -> A | LOC_Os12g35880-LOC_Os12g35890 | intergenic_region ; MODIFIER | silent_mutation | Average:26.225; most accessible tissue: Callus, score: 57.635 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1221867400 | NA | 1.18E-06 | mr1236 | 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 |
| vg1221867400 | 4.79E-06 | 4.78E-06 | mr1562 | 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 |
| vg1221867400 | NA | 1.46E-06 | mr1559_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 |
| vg1221867400 | NA | 1.36E-08 | mr1676_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 |