| Variant ID: vg1224806805 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 24806805 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.10, others allele: 0.00, population size: 97. )
AATCATTTCAGCAAATAAAAAAAATCCGCATCACCCCTCCCAGCCGACATCACTGCGGGCCTCCCCCTCTGGCCGATGGCTCTCCTCCTCCGTCCTCTGC[C/T]
GCTGCTCGAGGGGAGCACCGCCTCCGCCGCTGCCGCCGGAAATCTAAATTTAGTCCACCGTTCCTTTTTCTTTTCTTCAAGCCCAAATTGACAGCGTTAA
TTAACGCTGTCAATTTGGGCTTGAAGAAAAGAAAAAGGAACGGTGGACTAAATTTAGATTTCCGGCGGCAGCGGCGGAGGCGGTGCTCCCCTCGAGCAGC[G/A]
GCAGAGGACGGAGGAGGAGAGCCATCGGCCAGAGGGGGAGGCCCGCAGTGATGTCGGCTGGGAGGGGTGATGCGGATTTTTTTTATTTGCTGAAATGATT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 62.30% | 37.60% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 92.10% | 7.80% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 23.10% | 76.90% | 0.00% | 0.00% | NA |
| Aus | 269 | 1.10% | 98.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 86.90% | 12.90% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 92.30% | 7.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 91.50% | 8.30% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 3.90% | 96.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 58.70% | 41.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 9.50% | 90.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 54.40% | 45.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1224806805 | C -> T | LOC_Os12g40100-LOC_Os12g40115 | intergenic_region ; MODIFIER | silent_mutation | Average:53.709; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1224806805 | NA | 6.25E-12 | Grain_width | Jap_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 |
| vg1224806805 | NA | 1.31E-13 | mr1013 | 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 |
| vg1224806805 | NA | 2.49E-13 | mr1270 | 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 |
| vg1224806805 | 1.43E-07 | 6.44E-20 | mr1334 | Jap_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 |
| vg1224806805 | NA | 4.30E-09 | mr1403 | 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 |
| vg1224806805 | NA | 1.41E-22 | mr1422 | 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 |
| vg1224806805 | NA | 2.20E-08 | mr1465 | 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 |
| vg1224806805 | NA | 8.52E-15 | mr1540 | 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 |
| vg1224806805 | NA | 8.34E-11 | mr1720 | 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 |
| vg1224806805 | NA | 7.06E-15 | mr1732 | 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 |
Address: Room B111, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural university, Wuhan, 430070, China
Comments or Questions? Please contact us. Our website: http://xielab.ncpgr.cn/