| Variant ID: vg1206630456 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 6630456 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GTTCTGTCGATGTTTTGCCACTGCAACCCATTGGTGGGGTGTCTCAGCATCCTGTCTTGTTGATGTTTTTCTGCGTGCCAACGCATTATTCTAGCATGCG[C/T]
TTTCTTCCTGAACAAACGCCTCAGCCATGGTATTATAGGGAAATAACACATCAACTTAGTTGGAACTCTCTTTTTTGAAGGTTGTCCGTCAACATCACCT
AGGTGATGTTGACGGACAACCTTCAAAAAAGAGAGTTCCAACTAAGTTGATGTGTTATTTCCCTATAATACCATGGCTGAGGCGTTTGTTCAGGAAGAAA[G/A]
CGCATGCTAGAATAATGCGTTGGCACGCAGAAAAACATCAACAAGACAGGATGCTGAGACACCCCACCAATGGGTTGCAGTGGCAAAACATCGACAGAAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.30% | 14.50% | 5.10% | 51.08% | NA |
| All Indica | 2759 | 4.40% | 9.80% | 8.30% | 77.49% | NA |
| All Japonica | 1512 | 75.50% | 21.00% | 0.07% | 3.37% | NA |
| Aus | 269 | 28.60% | 22.30% | 1.86% | 47.21% | NA |
| Indica I | 595 | 4.70% | 15.50% | 10.25% | 69.58% | NA |
| Indica II | 465 | 3.70% | 11.60% | 6.88% | 77.85% | NA |
| Indica III | 913 | 2.30% | 4.70% | 8.65% | 84.34% | NA |
| Indica Intermediate | 786 | 7.00% | 10.40% | 7.25% | 75.32% | NA |
| Temperate Japonica | 767 | 67.70% | 27.80% | 0.13% | 4.43% | NA |
| Tropical Japonica | 504 | 93.50% | 4.20% | 0.00% | 2.38% | NA |
| Japonica Intermediate | 241 | 63.10% | 34.90% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 3.10% | 20.80% | 6.25% | 69.79% | NA |
| Intermediate | 90 | 47.80% | 17.80% | 0.00% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1206630456 | C -> DEL | N | N | silent_mutation | Average:17.823; most accessible tissue: Callus, score: 35.346 | N | N | N | N |
| vg1206630456 | C -> T | LOC_Os12g12100.1 | upstream_gene_variant ; 892.0bp to feature; MODIFIER | silent_mutation | Average:17.823; most accessible tissue: Callus, score: 35.346 | N | N | N | N |
| vg1206630456 | C -> T | LOC_Os12g12090.1 | downstream_gene_variant ; 4414.0bp to feature; MODIFIER | silent_mutation | Average:17.823; most accessible tissue: Callus, score: 35.346 | N | N | N | N |
| vg1206630456 | C -> T | LOC_Os12g12100-LOC_Os12g12110 | intergenic_region ; MODIFIER | silent_mutation | Average:17.823; most accessible tissue: Callus, score: 35.346 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1206630456 | 1.13E-06 | NA | mr1149 | 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 |