| Variant ID: vg0505746038 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 5746038 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACTAGGGTCCGTATAGAGGACGTCGCTGTCGAGCGGTCACTGGTGGCGGCGGCCTCCGGCGCAAGGAGGCAAATGACAGCGGTGCGCCGCCTGCGGTGAC[G/A]
CGCAGCAACTATCTGGGGTGGAAGCGGACGGCGGAGGCGATGAGAGCAGGTTCCGCCACTGGATTGGAGGAGGAGGGCAGCGGCAGCGGACGGGAGGTGC
GCACCTCCCGTCCGCTGCCGCTGCCCTCCTCCTCCAATCCAGTGGCGGAACCTGCTCTCATCGCCTCCGCCGTCCGCTTCCACCCCAGATAGTTGCTGCG[C/T]
GTCACCGCAGGCGGCGCACCGCTGTCATTTGCCTCCTTGCGCCGGAGGCCGCCGCCACCAGTGACCGCTCGACAGCGACGTCCTCTATACGGACCCTAGT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.50% | 2.60% | 16.36% | 22.53% | NA |
| All Indica | 2759 | 64.40% | 0.30% | 22.40% | 12.90% | NA |
| All Japonica | 1512 | 49.80% | 7.40% | 5.03% | 37.76% | NA |
| Aus | 269 | 35.70% | 0.00% | 23.79% | 40.52% | NA |
| Indica I | 595 | 63.40% | 0.00% | 28.24% | 8.40% | NA |
| Indica II | 465 | 63.00% | 1.30% | 22.80% | 12.90% | NA |
| Indica III | 913 | 62.70% | 0.10% | 21.91% | 15.33% | NA |
| Indica Intermediate | 786 | 68.10% | 0.10% | 18.32% | 13.49% | NA |
| Temperate Japonica | 767 | 74.70% | 14.50% | 5.22% | 5.61% | NA |
| Tropical Japonica | 504 | 11.90% | 0.00% | 5.75% | 82.34% | NA |
| Japonica Intermediate | 241 | 49.80% | 0.40% | 2.90% | 46.89% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 1.04% | 7.29% | NA |
| Intermediate | 90 | 58.90% | 1.10% | 15.56% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0505746038 | G -> DEL | N | N | silent_mutation | Average:15.287; most accessible tissue: Callus, score: 66.214 | N | N | N | N |
| vg0505746038 | G -> A | LOC_Os05g10550.1 | upstream_gene_variant ; 3291.0bp to feature; MODIFIER | silent_mutation | Average:15.287; most accessible tissue: Callus, score: 66.214 | N | N | N | N |
| vg0505746038 | G -> A | LOC_Os05g10560.1 | upstream_gene_variant ; 1307.0bp to feature; MODIFIER | silent_mutation | Average:15.287; most accessible tissue: Callus, score: 66.214 | N | N | N | N |
| vg0505746038 | G -> A | LOC_Os05g10570.1 | upstream_gene_variant ; 3562.0bp to feature; MODIFIER | silent_mutation | Average:15.287; most accessible tissue: Callus, score: 66.214 | N | N | N | N |
| vg0505746038 | G -> A | LOC_Os05g10570.2 | upstream_gene_variant ; 3560.0bp to feature; MODIFIER | silent_mutation | Average:15.287; most accessible tissue: Callus, score: 66.214 | N | N | N | N |
| vg0505746038 | G -> A | LOC_Os05g10550-LOC_Os05g10560 | intergenic_region ; MODIFIER | silent_mutation | Average:15.287; most accessible tissue: Callus, score: 66.214 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0505746038 | 2.87E-07 | 3.23E-09 | Yield | Jap_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 |
| vg0505746038 | NA | 2.35E-06 | mr1627 | 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 |
| vg0505746038 | NA | 1.01E-06 | mr1627_2 | 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 |