| Variant ID: vg1016625606 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 16625606 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.72, G: 0.29, others allele: 0.00, population size: 200. )
CCACAATTGGCTGAGACAAGTGGTGGCATGCATGGCCATTTGTTGCGTCGGATGCTTCATCCTTGTGTGATCTAACCAACCAATGCAACGCTCTCTCCCT[T/G]
TGGATGCAACAGCATGCATGTTTTTAGCTAAAAGTCTTGTGTAAATATGTTATGTTTCTTAATTCTTACGTGTTTTCAGCTAGCATAAAGACAATGACTT
AAGTCATTGTCTTTATGCTAGCTGAAAACACGTAAGAATTAAGAAACATAACATATTTACACAAGACTTTTAGCTAAAAACATGCATGCTGTTGCATCCA[A/C]
AGGGAGAGAGCGTTGCATTGGTTGGTTAGATCACACAAGGATGAAGCATCCGACGCAACAAATGGCCATGCATGCCACCACTTGTCTCAGCCAATTGTGG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 68.00% | 31.70% | 0.15% | 0.11% | NA |
| All Indica | 2759 | 98.30% | 1.40% | 0.22% | 0.07% | NA |
| All Japonica | 1512 | 7.80% | 92.10% | 0.00% | 0.13% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.00% | 0.50% | 0.50% | 0.00% | NA |
| Indica II | 465 | 96.80% | 2.80% | 0.22% | 0.22% | NA |
| Indica III | 913 | 99.70% | 0.20% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 97.20% | 2.50% | 0.13% | 0.13% | NA |
| Temperate Japonica | 767 | 2.30% | 97.50% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 6.30% | 93.50% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 28.20% | 71.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 67.70% | 32.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 55.60% | 42.20% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1016625606 | T -> G | LOC_Os10g31710.1 | upstream_gene_variant ; 3903.0bp to feature; MODIFIER | silent_mutation | Average:52.407; most accessible tissue: Zhenshan97 young leaf, score: 80.589 | N | N | N | N |
| vg1016625606 | T -> G | LOC_Os10g31720.1 | downstream_gene_variant ; 213.0bp to feature; MODIFIER | silent_mutation | Average:52.407; most accessible tissue: Zhenshan97 young leaf, score: 80.589 | N | N | N | N |
| vg1016625606 | T -> G | LOC_Os10g31710-LOC_Os10g31720 | intergenic_region ; MODIFIER | silent_mutation | Average:52.407; most accessible tissue: Zhenshan97 young leaf, score: 80.589 | N | N | N | N |
| vg1016625606 | T -> DEL | N | N | silent_mutation | Average:52.407; most accessible tissue: Zhenshan97 young leaf, score: 80.589 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1016625606 | NA | 4.01E-10 | Grain_weight | All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1016625606 | NA | 3.63E-13 | mr1010 | 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 |
| vg1016625606 | NA | 8.53E-14 | mr1035 | 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 |
| vg1016625606 | NA | 1.12E-93 | mr1071 | 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 |
| vg1016625606 | NA | 9.00E-85 | mr1080 | 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 |
| vg1016625606 | NA | 1.04E-06 | mr1080 | 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 |
| vg1016625606 | NA | 6.72E-96 | mr1140 | 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 |
| vg1016625606 | NA | 5.03E-07 | mr1140 | 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 |
| vg1016625606 | NA | 2.42E-07 | mr1162 | 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 |
| vg1016625606 | NA | 3.07E-10 | mr1191 | 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 |
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