| Variant ID: vg1016355947 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 16355947 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.00, others allele: 0.00, population size: 204. )
CTGATCTGTGCGAAATGAATGGCGTGTAGACTAAAGGGGGAAAGAAATATTTCATGACACTGATAGATGATTGCACTAGATTCTGCTATGTGTACCTATT[A/G]
AAAACAAAGGATGAAGCATTACATTACTTTAAGATATATATGGCTGAGGTAGAAAACCAGCTGGAAAGGAAAATCAAACGGTTGAGGTCTGATAGGGGTG
CACCCCTATCAGACCTCAACCGTTTGATTTTCCTTTCCAGCTGGTTTTCTACCTCAGCCATATATATCTTAAAGTAATGTAATGCTTCATCCTTTGTTTT[T/C]
AATAGGTACACATAGCAGAATCTAGTGCAATCATCTATCAGTGTCATGAAATATTTCTTTCCCCCTTTAGTCTACACGCCATTCATTTCGCACAGATCAG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.90% | 10.30% | 1.21% | 39.61% | NA |
| All Indica | 2759 | 27.70% | 7.10% | 1.34% | 63.86% | NA |
| All Japonica | 1512 | 94.90% | 0.90% | 0.93% | 3.31% | NA |
| Aus | 269 | 21.20% | 76.60% | 0.00% | 2.23% | NA |
| Indica I | 595 | 16.50% | 17.60% | 1.01% | 64.87% | NA |
| Indica II | 465 | 24.90% | 1.70% | 1.51% | 71.83% | NA |
| Indica III | 913 | 33.20% | 5.00% | 0.99% | 60.79% | NA |
| Indica Intermediate | 786 | 31.30% | 4.80% | 1.91% | 61.96% | NA |
| Temperate Japonica | 767 | 98.70% | 0.10% | 0.26% | 0.91% | NA |
| Tropical Japonica | 504 | 94.40% | 1.20% | 0.99% | 3.37% | NA |
| Japonica Intermediate | 241 | 83.80% | 2.50% | 2.90% | 10.79% | NA |
| VI/Aromatic | 96 | 9.40% | 63.50% | 3.12% | 23.96% | NA |
| Intermediate | 90 | 51.10% | 11.10% | 3.33% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1016355947 | A -> G | LOC_Os10g31200.1 | upstream_gene_variant ; 349.0bp to feature; MODIFIER | silent_mutation | Average:24.178; most accessible tissue: Zhenshan97 young leaf, score: 41.875 | N | N | N | N |
| vg1016355947 | A -> G | LOC_Os10g31189.1 | downstream_gene_variant ; 72.0bp to feature; MODIFIER | silent_mutation | Average:24.178; most accessible tissue: Zhenshan97 young leaf, score: 41.875 | N | N | N | N |
| vg1016355947 | A -> G | LOC_Os10g31189-LOC_Os10g31200 | intergenic_region ; MODIFIER | silent_mutation | Average:24.178; most accessible tissue: Zhenshan97 young leaf, score: 41.875 | N | N | N | N |
| vg1016355947 | A -> DEL | N | N | silent_mutation | Average:24.178; most accessible tissue: Zhenshan97 young leaf, score: 41.875 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1016355947 | 4.86E-06 | NA | Plant_height | Ind_All | YES | 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 |
| vg1016355947 | NA | 3.73E-06 | mr1006 | 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 |
| vg1016355947 | NA | 2.22E-06 | mr1052 | 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 |
| vg1016355947 | NA | 5.08E-09 | mr1166_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 |
| vg1016355947 | NA | 6.51E-06 | mr1219_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 |