| Variant ID: vg1107500708 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 7500708 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GAAATATTGATTTGAGAATTTGGAGACTATTCGGGGATGATTGATTTAGGATTTTGGGATAGGATAGAGTGAATCAATTAATTAAAAACAATGAAGAAAA[G/A]
AATAGAATAAAGTAGCAATCGGAGCTAGCCAGCTAGCCTCTTTAGTCCCGATTACCTACTCTATCTTTAGTCCCGGTTGGTGCTAAAAATAGATTTTTAC
GTAAAAATCTATTTTTAGCACCAACCGGGACTAAAGATAGAGTAGGTAATCGGGACTAAAGAGGCTAGCTGGCTAGCTCCGATTGCTACTTTATTCTATT[C/T]
TTTTCTTCATTGTTTTTAATTAATTGATTCACTCTATCCTATCCCAAAATCCTAAATCAATCATCCCCGAATAGTCTCCAAATTCTCAAATCAATATTTC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.80% | 24.10% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 95.50% | 4.40% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 51.30% | 48.60% | 0.13% | 0.00% | NA |
| Aus | 269 | 10.00% | 89.60% | 0.37% | 0.00% | NA |
| Indica I | 595 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.60% | 0.22% | 0.00% | NA |
| Indica III | 913 | 94.50% | 5.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 92.20% | 7.60% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 63.40% | 36.60% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 26.60% | 73.20% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 64.30% | 35.30% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 75.00% | 25.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 18.90% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1107500708 | G -> A | LOC_Os11g13680.1 | downstream_gene_variant ; 1720.0bp to feature; MODIFIER | silent_mutation | Average:39.361; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | N | N | N | N |
| vg1107500708 | G -> A | LOC_Os11g13670-LOC_Os11g13680 | intergenic_region ; MODIFIER | silent_mutation | Average:39.361; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1107500708 | 5.00E-07 | NA | mr1543 | 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 |
| vg1107500708 | NA | 3.70E-06 | mr1990 | 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 |