| Variant ID: vg1206605318 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 6605318 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TATCCAATGTTACTATATGGTTATCCTTTTATGTATTATATGCCATGGATGCCTCAACCACCTATGCCGTGTCATCAAGCATGGAAGCAATCACCTAGGA[C/T]
GGTACCAAGTCATTCTAACTCAAGACAAGACCGTTTCCCACGAAAGAATCGGTCAAGTGGATCAAAAGTGAAAAATGTGAAGAAGTTGTGGGTGAGAAAA
TTTTCTCACCCACAACTTCTTCACATTTTTCACTTTTGATCCACTTGACCGATTCTTTCGTGGGAAACGGTCTTGTCTTGAGTTAGAATGACTTGGTACC[G/A]
TCCTAGGTGATTGCTTCCATGCTTGATGACACGGCATAGGTGGTTGAGGCATCCATGGCATATAATACATAAAAGGATAACCATATAGTAACATTGGATA
| 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 | 93.90% | 0.80% | 2.73% | 2.52% | NA |
| All Indica | 2759 | 92.00% | 1.10% | 3.70% | 3.26% | NA |
| All Japonica | 1512 | 98.10% | 0.10% | 0.33% | 1.52% | NA |
| Aus | 269 | 92.20% | 1.90% | 5.95% | 0.00% | NA |
| Indica I | 595 | 90.10% | 0.70% | 4.54% | 4.71% | NA |
| Indica II | 465 | 98.10% | 0.40% | 0.86% | 0.65% | NA |
| Indica III | 913 | 89.60% | 1.60% | 4.82% | 3.94% | NA |
| Indica Intermediate | 786 | 92.60% | 1.00% | 3.44% | 2.93% | NA |
| Temperate Japonica | 767 | 96.70% | 0.00% | 0.39% | 2.87% | NA |
| Tropical Japonica | 504 | 99.20% | 0.20% | 0.40% | 0.20% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 88.50% | 5.20% | 4.17% | 2.08% | NA |
| Intermediate | 90 | 93.30% | 0.00% | 2.22% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1206605318 | C -> DEL | N | N | silent_mutation | Average:8.028; most accessible tissue: Callus, score: 15.168 | N | N | N | N |
| vg1206605318 | C -> T | LOC_Os12g12060.1 | downstream_gene_variant ; 3247.0bp to feature; MODIFIER | silent_mutation | Average:8.028; most accessible tissue: Callus, score: 15.168 | N | N | N | N |
| vg1206605318 | C -> T | LOC_Os12g12040-LOC_Os12g12060 | intergenic_region ; MODIFIER | silent_mutation | Average:8.028; most accessible tissue: Callus, score: 15.168 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1206605318 | 7.43E-06 | 7.44E-06 | mr1187 | Ind_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 |
| vg1206605318 | 1.49E-06 | 4.59E-06 | mr1245 | Ind_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 |
| vg1206605318 | NA | 3.83E-06 | mr1319 | Ind_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 |
| vg1206605318 | 1.74E-06 | 1.74E-06 | mr1323 | Ind_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 |
| vg1206605318 | NA | 1.02E-06 | mr1921 | Ind_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 |