| Variant ID: vg1219197044 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 19197044 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTCGCGGGATGCACTGGAAGACATACAACGCTTGCCACAAGCGGGAATGGGTAACTGCCTGACTTGAAGTATAGCTTTCCTCTGGCTGATGTTCCCAGGC[A/T]
AGGGTGAGCATGATGGAGTTGGGTCGGCTGGGGTGTCCGGTTGTCCAGCTGTCGGATTCACCGCGGCGCACGAGGGGACTGCCCACCTCCGGGGTAGGGG
CCCCTACCCCGGAGGTGGGCAGTCCCCTCGTGCGCCGCGGTGAATCCGACAGCTGGACAACCGGACACCCCAGCCGACCCAACTCCATCATGCTCACCCT[T/A]
GCCTGGGAACATCAGCCAGAGGAAAGCTATACTTCAAGTCAGGCAGTTACCCATTCCCGCTTGTGGCAAGCGTTGTATGTCTTCCAGTGCATCCCGCGAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.80% | 3.10% | 12.91% | 6.20% | NA |
| All Indica | 2759 | 66.70% | 4.90% | 20.08% | 8.41% | NA |
| All Japonica | 1512 | 98.10% | 0.00% | 0.46% | 1.46% | NA |
| Aus | 269 | 70.60% | 3.00% | 15.61% | 10.78% | NA |
| Indica I | 595 | 65.00% | 2.90% | 27.39% | 4.71% | NA |
| Indica II | 465 | 64.90% | 2.20% | 22.37% | 10.54% | NA |
| Indica III | 913 | 70.80% | 7.10% | 13.91% | 8.21% | NA |
| Indica Intermediate | 786 | 64.10% | 5.30% | 20.36% | 10.18% | NA |
| Temperate Japonica | 767 | 99.00% | 0.00% | 0.39% | 0.65% | NA |
| Tropical Japonica | 504 | 98.60% | 0.00% | 0.00% | 1.39% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.00% | 1.66% | 4.15% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 4.17% | 1.04% | NA |
| Intermediate | 90 | 82.20% | 4.40% | 3.33% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1219197044 | A -> DEL | N | N | silent_mutation | Average:17.479; most accessible tissue: Minghui63 root, score: 43.505 | N | N | N | N |
| vg1219197044 | A -> T | LOC_Os12g31870.1 | upstream_gene_variant ; 1011.0bp to feature; MODIFIER | silent_mutation | Average:17.479; most accessible tissue: Minghui63 root, score: 43.505 | N | N | N | N |
| vg1219197044 | A -> T | LOC_Os12g31880.1 | upstream_gene_variant ; 2245.0bp to feature; MODIFIER | silent_mutation | Average:17.479; most accessible tissue: Minghui63 root, score: 43.505 | N | N | N | N |
| vg1219197044 | A -> T | LOC_Os12g31870-LOC_Os12g31880 | intergenic_region ; MODIFIER | silent_mutation | Average:17.479; most accessible tissue: Minghui63 root, score: 43.505 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1219197044 | 2.50E-06 | NA | mr1172_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 |