| Variant ID: vg0514815080 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 14815080 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 259. )
TCATAAATATTCAACCTACTTGCGCTGTCACCGAAGCAACATCTAGCTTAATTGTTAATACTGCATGATGGCAAAGTTTTGTAGTTGTGGAGACATACTT[C/A]
AGGAATTAGGATGCTGCTTACTCAACTTCGAGATTGCATTGCGAAATTCTGCAGCACTTCTTTTTTTAAGGTATACTACCTGAGGTGACAGATACTTCCA
TGGAAGTATCTGTCACCTCAGGTAGTATACCTTAAAAAAAGAAGTGCTGCAGAATTTCGCAATGCAATCTCGAAGTTGAGTAAGCAGCATCCTAATTCCT[G/T]
AAGTATGTCTCCACAACTACAAAACTTTGCCATCATGCAGTATTAACAATTAAGCTAGATGTTGCTTCGGTGACAGCGCAAGTAGGTTGAATATTTATGA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.30% | 9.10% | 2.62% | 0.00% | NA |
| All Indica | 2759 | 81.00% | 14.80% | 4.24% | 0.00% | NA |
| All Japonica | 1512 | 98.70% | 1.00% | 0.26% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 71.40% | 17.10% | 11.43% | 0.00% | NA |
| Indica II | 465 | 74.40% | 22.20% | 3.44% | 0.00% | NA |
| Indica III | 913 | 92.00% | 7.80% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 79.40% | 16.70% | 3.94% | 0.00% | NA |
| Temperate Japonica | 767 | 98.30% | 1.60% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.20% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.80% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 10.00% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0514815080 | C -> A | LOC_Os05g25480.1 | upstream_gene_variant ; 1183.0bp to feature; MODIFIER | silent_mutation | Average:62.997; most accessible tissue: Minghui63 root, score: 78.833 | N | N | N | N |
| vg0514815080 | C -> A | LOC_Os05g25470-LOC_Os05g25480 | intergenic_region ; MODIFIER | silent_mutation | Average:62.997; most accessible tissue: Minghui63 root, score: 78.833 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0514815080 | NA | 8.38E-06 | mr1578_2 | 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 |
| vg0514815080 | 3.16E-06 | NA | mr1647_2 | Ind_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 |