| Variant ID: vg1210252343 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 10252343 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TACAGATTCACGGATTTAGTTTCCACCGGCCAACACGCAGAACGTACGACTCGCCTCCACACACTCGTGCTTGTGCCCGCAATACATTTTTTTAAAAAAT[G/A]
TACAAATGGATAGCAAACCGAGGAGCCATTTCTAAAAAAAAACAGCAAAAAAAAAAGATTTAAGCACCATATATAGAGAGGCCTCCACACTGCTAGATTT
AAATCTAGCAGTGTGGAGGCCTCTCTATATATGGTGCTTAAATCTTTTTTTTTTGCTGTTTTTTTTTAGAAATGGCTCCTCGGTTTGCTATCCATTTGTA[C/T]
ATTTTTTAAAAAAATGTATTGCGGGCACAAGCACGAGTGTGTGGAGGCGAGTCGTACGTTCTGCGTGTTGGCCGGTGGAAACTAAATCCGTGAATCTGTA
| 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 | 86.50% | 1.10% | 10.39% | 1.95% | NA |
| All Indica | 2759 | 84.70% | 1.00% | 11.53% | 2.75% | NA |
| All Japonica | 1512 | 99.50% | 0.10% | 0.40% | 0.00% | NA |
| Aus | 269 | 44.20% | 7.80% | 42.75% | 5.20% | NA |
| Indica I | 595 | 56.00% | 3.00% | 32.44% | 8.57% | NA |
| Indica II | 465 | 95.70% | 0.20% | 3.23% | 0.86% | NA |
| Indica III | 913 | 96.30% | 0.30% | 3.07% | 0.33% | NA |
| Indica Intermediate | 786 | 86.60% | 0.60% | 10.43% | 2.29% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.40% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 50.00% | 3.10% | 44.79% | 2.08% | NA |
| Intermediate | 90 | 88.90% | 1.10% | 10.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1210252343 | G -> DEL | N | N | silent_mutation | Average:66.036; most accessible tissue: Zhenshan97 young leaf, score: 87.723 | N | N | N | N |
| vg1210252343 | G -> A | LOC_Os12g17880.1 | downstream_gene_variant ; 1738.0bp to feature; MODIFIER | silent_mutation | Average:66.036; most accessible tissue: Zhenshan97 young leaf, score: 87.723 | N | N | N | N |
| vg1210252343 | G -> A | LOC_Os12g17860-LOC_Os12g17880 | intergenic_region ; MODIFIER | silent_mutation | Average:66.036; most accessible tissue: Zhenshan97 young leaf, score: 87.723 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1210252343 | 6.17E-06 | NA | mr1020 | 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 |
| vg1210252343 | 7.29E-06 | NA | mr1021 | 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 |
| vg1210252343 | 5.99E-06 | NA | mr1032 | 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 |
| vg1210252343 | NA | 6.82E-07 | mr1706 | 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 |
| vg1210252343 | NA | 5.94E-06 | mr1864_2 | 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 |