| Variant ID: vg1222257972 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22257972 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATTTGCTGTATGAAGAGAATATTGCCCATAGCAGGTCTCATTACCAATTCTTATTGGTTGTATGTGACACTTATGTGAGTATCCATGGATATATGGGGAT[A/G]
TGCAATTCTCTTATGCTTCTATTCTTTGATATGGGCATGACTCTTTCATTTTACCGACGTTGGTGTGCACTCCAACTGCTGGTTTTCTTCCTTGATAGGA
TCCTATCAAGGAAGAAAACCAGCAGTTGGAGTGCACACCAACGTCGGTAAAATGAAAGAGTCATGCCCATATCAAAGAATAGAAGCATAAGAGAATTGCA[T/C]
ATCCCCATATATCCATGGATACTCACATAAGTGTCACATACAACCAATAAGAATTGGTAATGAGACCTGCTATGGGCAATATTCTCTTCATACAGCAAAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.20% | 19.30% | 1.44% | 14.16% | NA |
| All Indica | 2759 | 75.70% | 5.70% | 1.96% | 16.67% | NA |
| All Japonica | 1512 | 48.00% | 39.30% | 0.53% | 12.17% | NA |
| Aus | 269 | 80.70% | 11.90% | 2.23% | 5.20% | NA |
| Indica I | 595 | 80.80% | 8.40% | 0.67% | 10.08% | NA |
| Indica II | 465 | 84.50% | 2.40% | 1.51% | 11.61% | NA |
| Indica III | 913 | 71.20% | 5.40% | 1.97% | 21.47% | NA |
| Indica Intermediate | 786 | 71.80% | 6.00% | 3.18% | 19.08% | NA |
| Temperate Japonica | 767 | 75.00% | 16.40% | 0.52% | 8.08% | NA |
| Tropical Japonica | 504 | 18.30% | 63.90% | 0.60% | 17.26% | NA |
| Japonica Intermediate | 241 | 24.50% | 60.60% | 0.41% | 14.52% | NA |
| VI/Aromatic | 96 | 4.20% | 93.80% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 48.90% | 41.10% | 0.00% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222257972 | A -> DEL | N | N | silent_mutation | Average:34.596; most accessible tissue: Callus, score: 51.477 | N | N | N | N |
| vg1222257972 | A -> G | LOC_Os12g36350.1 | downstream_gene_variant ; 3237.0bp to feature; MODIFIER | silent_mutation | Average:34.596; most accessible tissue: Callus, score: 51.477 | N | N | N | N |
| vg1222257972 | A -> G | LOC_Os12g36360.1 | downstream_gene_variant ; 2234.0bp to feature; MODIFIER | silent_mutation | Average:34.596; most accessible tissue: Callus, score: 51.477 | N | N | N | N |
| vg1222257972 | A -> G | LOC_Os12g36350-LOC_Os12g36360 | intergenic_region ; MODIFIER | silent_mutation | Average:34.596; most accessible tissue: Callus, score: 51.477 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1222257972 | NA | 9.41E-07 | mr1278_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 |
| vg1222257972 | NA | 1.86E-06 | mr1329_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 |
| vg1222257972 | NA | 5.52E-06 | mr1982_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 |
| vg1222257972 | 3.80E-06 | 3.80E-06 | mr1983_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 |