| Variant ID: vg0324095158 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 24095158 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATACGTCGTCTCCGAGAGAAATCCACACTGTTACACAGTGTTTTAAATACTAACCGTCGTCCCCGAGAAACTTCACCCTGTTACTTCCGTTTTCACCGCT[T/A]
AAGCCAACTTTGTCCTCTCTCTCTCCGGCGATTTCTTCGACGTGCAAGGCGATCCCCTCTCCGGCCAGATTTCCGCCTGCGGCGATGTCGTCCTCCGCCA
TGGCGGAGGACGACATCGCCGCAGGCGGAAATCTGGCCGGAGAGGGGATCGCCTTGCACGTCGAAGAAATCGCCGGAGAGAGAGAGGACAAAGTTGGCTT[A/T]
AGCGGTGAAAACGGAAGTAACAGGGTGAAGTTTCTCGGGGACGACGGTTAGTATTTAAAACACTGTGTAACAGTGTGGATTTCTCTCGGAGACGACGTAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.10% | 3.30% | 3.17% | 54.42% | NA |
| All Indica | 2759 | 7.50% | 0.30% | 2.61% | 89.63% | NA |
| All Japonica | 1512 | 85.10% | 10.00% | 4.30% | 0.66% | NA |
| Aus | 269 | 83.30% | 0.00% | 3.35% | 13.38% | NA |
| Indica I | 595 | 8.40% | 0.00% | 2.02% | 89.58% | NA |
| Indica II | 465 | 3.70% | 1.10% | 3.01% | 92.26% | NA |
| Indica III | 913 | 4.40% | 0.00% | 2.19% | 93.43% | NA |
| Indica Intermediate | 786 | 12.70% | 0.30% | 3.31% | 83.72% | NA |
| Temperate Japonica | 767 | 73.00% | 19.60% | 7.04% | 0.39% | NA |
| Tropical Japonica | 504 | 97.80% | 0.00% | 1.19% | 0.99% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.40% | 2.07% | 0.83% | NA |
| VI/Aromatic | 96 | 82.30% | 0.00% | 2.08% | 15.62% | NA |
| Intermediate | 90 | 55.60% | 0.00% | 2.22% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0324095158 | T -> A | LOC_Os03g43210.1 | upstream_gene_variant ; 85.0bp to feature; MODIFIER | silent_mutation | Average:6.769; most accessible tissue: Zhenshan97 young leaf, score: 16.166 | N | N | N | N |
| vg0324095158 | T -> A | LOC_Os03g43200.1 | downstream_gene_variant ; 1642.0bp to feature; MODIFIER | silent_mutation | Average:6.769; most accessible tissue: Zhenshan97 young leaf, score: 16.166 | N | N | N | N |
| vg0324095158 | T -> A | LOC_Os03g43220.1 | downstream_gene_variant ; 3614.0bp to feature; MODIFIER | silent_mutation | Average:6.769; most accessible tissue: Zhenshan97 young leaf, score: 16.166 | N | N | N | N |
| vg0324095158 | T -> A | LOC_Os03g43200-LOC_Os03g43210 | intergenic_region ; MODIFIER | silent_mutation | Average:6.769; most accessible tissue: Zhenshan97 young leaf, score: 16.166 | N | N | N | N |
| vg0324095158 | T -> DEL | N | N | silent_mutation | Average:6.769; most accessible tissue: Zhenshan97 young leaf, score: 16.166 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0324095158 | 1.98E-06 | NA | mr1570 | 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 |
| vg0324095158 | 2.59E-06 | 2.92E-07 | mr1570 | 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 |
| vg0324095158 | NA | 3.42E-06 | mr1697 | 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 |