| Variant ID: vg0417712235 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 17712235 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.04, others allele: 0.00, population size: 68. )
GCATCTTAAGGATCTACACGCAAAAATGAGAGGATGATTTTTTCAGACGCGGTCAGTTATGGGCCGTCTGGAATCTGACGAGGGGTTCATCCAGGAAAAT[C/T]
GTTTTTTAGGAGTGCATGATTTGTTTGCTGCAAAATAGCATAGTCCACATGATTTTGTTCTCGAAATTTTTCTATATCTTCCACATATGGTAGAGGAAAT
ATTTCCTCTACCATATGTGGAAGATATAGAAAAATTTCGAGAACAAAATCATGTGGACTATGCTATTTTGCAGCAAACAAATCATGCACTCCTAAAAAAC[G/A]
ATTTTCCTGGATGAACCCCTCGTCAGATTCCAGACGGCCCATAACTGACCGCGTCTGAAAAAATCATCCTCTCATTTTTGCGTGTAGATCCTTAAGATGC
| 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 | 44.60% | 15.30% | 1.02% | 39.06% | NA |
| All Indica | 2759 | 38.50% | 10.90% | 1.23% | 49.44% | NA |
| All Japonica | 1512 | 47.90% | 26.90% | 0.73% | 24.54% | NA |
| Aus | 269 | 67.30% | 0.00% | 0.00% | 32.71% | NA |
| Indica I | 595 | 67.20% | 8.90% | 0.84% | 23.03% | NA |
| Indica II | 465 | 20.60% | 32.90% | 1.08% | 45.38% | NA |
| Indica III | 913 | 28.00% | 0.20% | 0.88% | 70.87% | NA |
| Indica Intermediate | 786 | 39.30% | 11.70% | 2.04% | 46.95% | NA |
| Temperate Japonica | 767 | 12.00% | 45.60% | 1.17% | 41.20% | NA |
| Tropical Japonica | 504 | 91.70% | 7.30% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 70.50% | 7.90% | 0.83% | 20.75% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 56.70% | 20.00% | 3.33% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0417712235 | C -> DEL | N | N | silent_mutation | Average:28.619; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |
| vg0417712235 | C -> T | LOC_Os04g29700-LOC_Os04g29730 | intergenic_region ; MODIFIER | silent_mutation | Average:28.619; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0417712235 | NA | 1.06E-17 | Plant_height | 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 |
| vg0417712235 | NA | 5.53E-07 | mr1851 | 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 |
| vg0417712235 | NA | 8.48E-06 | mr1864 | 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 |
| vg0417712235 | NA | 6.66E-07 | mr1060_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 |
| vg0417712235 | NA | 2.33E-06 | mr1296_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 |
| vg0417712235 | 4.42E-06 | 2.63E-07 | mr1749_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 |