| Variant ID: vg0506146864 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 6146864 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.68, T: 0.32, others allele: 0.00, population size: 94. )
ACTCGTCACCAACCCATCTGTAGCACCAACTTCCTTGTCGTGTCGCCGTCGACAAATCCGTTGGCGAGAAGGAAGGGAGAGGCGCCCGCTACTGCCGCCG[T/C]
GGCGTCTTCTCCCATGCGGCGCAGGCGAAGCGGGGGAGGGCGAGCGGCGCCAACGATGGGGAAAGGGGAGAGCAACACAGGATTAGGGAAGAAGAGCCGT
ACGGCTCTTCTTCCCTAATCCTGTGTTGCTCTCCCCTTTCCCCATCGTTGGCGCCGCTCGCCCTCCCCCGCTTCGCCTGCGCCGCATGGGAGAAGACGCC[A/G]
CGGCGGCAGTAGCGGGCGCCTCTCCCTTCCTTCTCGCCAACGGATTTGTCGACGGCGACACGACAAGGAAGTTGGTGCTACAGATGGGTTGGTGACGAGT
| 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 | 65.30% | 34.30% | 0.11% | 0.25% | NA |
| All Indica | 2759 | 61.20% | 38.30% | 0.07% | 0.43% | NA |
| All Japonica | 1512 | 80.80% | 19.10% | 0.07% | 0.00% | NA |
| Aus | 269 | 10.00% | 90.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 30.30% | 69.20% | 0.00% | 0.50% | NA |
| Indica II | 465 | 65.80% | 33.30% | 0.00% | 0.86% | NA |
| Indica III | 913 | 79.60% | 20.20% | 0.00% | 0.22% | NA |
| Indica Intermediate | 786 | 60.40% | 38.90% | 0.25% | 0.38% | NA |
| Temperate Japonica | 767 | 71.30% | 28.60% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 91.90% | 8.10% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 88.00% | 12.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 85.40% | 14.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 76.70% | 21.10% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0506146864 | T -> DEL | N | N | silent_mutation | Average:72.797; most accessible tissue: Zhenshan97 young leaf, score: 87.004 | N | N | N | N |
| vg0506146864 | T -> C | LOC_Os05g10990.1 | downstream_gene_variant ; 1973.0bp to feature; MODIFIER | silent_mutation | Average:72.797; most accessible tissue: Zhenshan97 young leaf, score: 87.004 | N | N | N | N |
| vg0506146864 | T -> C | LOC_Os05g10980-LOC_Os05g10990 | intergenic_region ; MODIFIER | silent_mutation | Average:72.797; most accessible tissue: Zhenshan97 young leaf, score: 87.004 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0506146864 | 3.95E-07 | 5.28E-15 | Grain_width | Ind_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 |
| vg0506146864 | NA | 4.14E-06 | mr1648 | 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 |
| vg0506146864 | 3.52E-06 | 4.51E-07 | mr1923 | 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 |