| Variant ID: vg1207495052 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 7495052 |
| Reference Allele: T | Alternative Allele: G,A |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AAAACCGGGACTACAATGAGTTACCAATCGGGAGTAAAAAGCATTTCTCTACCAGTGATACTTTTATGTATATATATAGTTTTATATATTTCAAAAAAAA[T/G,A]
TTAAATAAGTCGAATGGTCAAACATGCTTAAAAAAAGTCCACGACGTCCCATATTTACTATTTAGGGACAGAGGGACTACGCTATATAGAAATACTCGCA
TGCGAGTATTTCTATATAGCGTAGTCCCTCTGTCCCTAAATAGTAAATATGGGACGTCGTGGACTTTTTTTAAGCATGTTTGACCATTCGACTTATTTAA[A/C,T]
TTTTTTTTGAAATATATAAAACTATATATATACATAAAAGTATCACTGGTAGAGAAATGCTTTTTACTCCCGATTGGTAACTCATTGTAGTCCCGGTTTT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.40% | 5.00% | 0.25% | 0.74% | A: 0.66% |
| All Indica | 2759 | 90.90% | 7.60% | 0.07% | 0.40% | A: 1.01% |
| All Japonica | 1512 | 97.80% | 0.10% | 0.46% | 1.46% | A: 0.13% |
| Aus | 269 | 92.60% | 7.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 83.90% | 16.10% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.10% | 0.00% | 0.22% | 1.72% | NA |
| Indica III | 913 | 91.20% | 5.80% | 0.00% | 0.00% | A: 2.96% |
| Indica Intermediate | 786 | 91.50% | 7.90% | 0.13% | 0.38% | A: 0.13% |
| Temperate Japonica | 767 | 96.20% | 0.30% | 0.78% | 2.61% | A: 0.13% |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.20% | 0.20% | A: 0.20% |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 1.04% | 0.00% | A: 1.04% |
| Intermediate | 90 | 94.40% | 1.10% | 2.22% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1207495052 | T -> A | LOC_Os12g13400.1 | upstream_gene_variant ; 1533.0bp to feature; MODIFIER | silent_mutation | Average:38.562; most accessible tissue: Zhenshan97 young leaf, score: 57.159 | N | N | N | N |
| vg1207495052 | T -> A | LOC_Os12g13390-LOC_Os12g13400 | intergenic_region ; MODIFIER | silent_mutation | Average:38.562; most accessible tissue: Zhenshan97 young leaf, score: 57.159 | N | N | N | N |
| vg1207495052 | T -> DEL | N | N | silent_mutation | Average:38.562; most accessible tissue: Zhenshan97 young leaf, score: 57.159 | N | N | N | N |
| vg1207495052 | T -> G | LOC_Os12g13400.1 | upstream_gene_variant ; 1533.0bp to feature; MODIFIER | silent_mutation | Average:38.562; most accessible tissue: Zhenshan97 young leaf, score: 57.159 | N | N | N | N |
| vg1207495052 | T -> G | LOC_Os12g13390-LOC_Os12g13400 | intergenic_region ; MODIFIER | silent_mutation | Average:38.562; most accessible tissue: Zhenshan97 young leaf, score: 57.159 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1207495052 | NA | 8.55E-06 | mr1397 | 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 |
| vg1207495052 | 4.14E-06 | 4.14E-06 | mr1688 | 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 |
| vg1207495052 | NA | 2.99E-06 | mr1857 | 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 |