| Variant ID: vg1222205675 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22205675 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACCTTCCTCCCCATTAACGTTCAGCATGACGTGGCGTTTCAGTTGGCGGGGATTCTTGGTTGCTCCATAGCTTCCTTCCCCCAACCTTATTTATGCCTCC[C/T]
TCTCTCTGTTTGTTACCAAGCTTTGTCTTGCAAACTGTCAACCTCTCATCGCTAGGATTGACAAGCGACTTGCCGGTTGGCGCGGTCACCTTCTGTCTTC
GAAGACAGAAGGTGACCGCGCCAACCGGCAAGTCGCTTGTCAATCCTAGCGATGAGAGGTTGACAGTTTGCAAGACAAAGCTTGGTAACAAACAGAGAGA[G/A]
GGAGGCATAAATAAGGTTGGGGGAAGGAAGCTATGGAGCAACCAAGAATCCCCGCCAACTGAAACGCCACGTCATGCTGAACGTTAATGGGGAGGAAGGT
| 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 | 91.20% | 0.50% | 2.24% | 5.99% | NA |
| All Indica | 2759 | 92.80% | 0.00% | 2.46% | 4.78% | NA |
| All Japonica | 1512 | 87.80% | 1.60% | 2.31% | 8.33% | NA |
| Aus | 269 | 91.40% | 0.00% | 0.74% | 7.81% | NA |
| Indica I | 595 | 98.70% | 0.00% | 1.01% | 0.34% | NA |
| Indica II | 465 | 82.60% | 0.00% | 0.43% | 16.99% | NA |
| Indica III | 913 | 93.80% | 0.00% | 3.61% | 2.63% | NA |
| Indica Intermediate | 786 | 93.10% | 0.00% | 3.44% | 3.44% | NA |
| Temperate Japonica | 767 | 89.70% | 3.10% | 4.17% | 3.00% | NA |
| Tropical Japonica | 504 | 81.30% | 0.00% | 0.20% | 18.45% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.00% | 0.83% | 4.15% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 1.10% | 0.00% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222205675 | C -> DEL | N | N | silent_mutation | Average:65.94; most accessible tissue: Callus, score: 88.69 | N | N | N | N |
| vg1222205675 | C -> T | LOC_Os12g36240.1 | upstream_gene_variant ; 2235.0bp to feature; MODIFIER | silent_mutation | Average:65.94; most accessible tissue: Callus, score: 88.69 | N | N | N | N |
| vg1222205675 | C -> T | LOC_Os12g36230.1 | downstream_gene_variant ; 4156.0bp to feature; MODIFIER | silent_mutation | Average:65.94; most accessible tissue: Callus, score: 88.69 | N | N | N | N |
| vg1222205675 | C -> T | LOC_Os12g36250.1 | downstream_gene_variant ; 605.0bp to feature; MODIFIER | silent_mutation | Average:65.94; most accessible tissue: Callus, score: 88.69 | N | N | N | N |
| vg1222205675 | C -> T | LOC_Os12g36260.1 | downstream_gene_variant ; 2152.0bp to feature; MODIFIER | silent_mutation | Average:65.94; most accessible tissue: Callus, score: 88.69 | N | N | N | N |
| vg1222205675 | C -> T | LOC_Os12g36240-LOC_Os12g36250 | intergenic_region ; MODIFIER | silent_mutation | Average:65.94; most accessible tissue: Callus, score: 88.69 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1222205675 | 3.45E-06 | 3.45E-06 | mr1200 | 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 |
| vg1222205675 | 1.14E-06 | 1.61E-06 | mr1798 | 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 |