| Variant ID: vg1011166653 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 11166653 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CACCATTGCGTGTGTCAGGCGACGTGCAGCCCGACATATCCCATCAAATAATGATGGTGAGAGGTTATCATCCTCTTATCCCAGCCAGAGTCGGTCCTCC[C/T]
GCTCTGGTCAAAGCAAGGCTCCCGTTTCCCGGTGTAATAGGAGCCCAGAAGTCTTCACCCATTAAATGGTGACTGACATGGGCACCCCCCGTGTCAGGCG
CGCCTGACACGGGGGGTGCCCATGTCAGTCACCATTTAATGGGTGAAGACTTCTGGGCTCCTATTACACCGGGAAACGGGAGCCTTGCTTTGACCAGAGC[G/A]
GGAGGACCGACTCTGGCTGGGATAAGAGGATGATAACCTCTCACCATCATTATTTGATGGGATATGTCGGGCTGCACGTCGCCTGACACACGCAATGGTG
| 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 | 82.20% | 13.10% | 3.91% | 0.78% | NA |
| All Indica | 2759 | 98.60% | 0.70% | 0.36% | 0.33% | NA |
| All Japonica | 1512 | 51.60% | 38.50% | 9.92% | 0.00% | NA |
| Aus | 269 | 88.80% | 0.00% | 4.46% | 6.69% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.00% | 1.20% | 0.44% | 0.33% | NA |
| Indica Intermediate | 786 | 97.70% | 1.00% | 0.51% | 0.76% | NA |
| Temperate Japonica | 767 | 87.50% | 9.00% | 3.52% | 0.00% | NA |
| Tropical Japonica | 504 | 8.50% | 82.70% | 8.73% | 0.00% | NA |
| Japonica Intermediate | 241 | 27.40% | 39.80% | 32.78% | 0.00% | NA |
| VI/Aromatic | 96 | 81.20% | 3.10% | 8.33% | 7.29% | NA |
| Intermediate | 90 | 76.70% | 14.40% | 5.56% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1011166653 | C -> T | LOC_Os10g21770.1 | upstream_gene_variant ; 3895.0bp to feature; MODIFIER | silent_mutation | Average:46.554; most accessible tissue: Minghui63 young leaf, score: 71.839 | N | N | N | N |
| vg1011166653 | C -> T | LOC_Os10g21760.1 | downstream_gene_variant ; 576.0bp to feature; MODIFIER | silent_mutation | Average:46.554; most accessible tissue: Minghui63 young leaf, score: 71.839 | N | N | N | N |
| vg1011166653 | C -> T | LOC_Os10g21740-LOC_Os10g21760 | intergenic_region ; MODIFIER | silent_mutation | Average:46.554; most accessible tissue: Minghui63 young leaf, score: 71.839 | N | N | N | N |
| vg1011166653 | C -> DEL | N | N | silent_mutation | Average:46.554; most accessible tissue: Minghui63 young leaf, score: 71.839 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1011166653 | NA | 2.08E-07 | mr1180_2 | 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 |
| vg1011166653 | NA | 8.68E-06 | mr1419_2 | 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 |
| vg1011166653 | NA | 7.86E-08 | mr1668_2 | 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 |
| vg1011166653 | NA | 6.50E-10 | mr1761_2 | 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 |