Search for Variation information by Variation ID:
Detailed information for vg0515100790:
| Variant ID: vg0515100790 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 15100790 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 268. )
Flanking Sequence (100 bp) in Reference Genome:
AAATATGGATGCATGAAGACATACCATTCAAAAGATGCCCTTTACAAGACCATCACCGCTCATCCTAACAAGGATGGACACGGGCTCGGGTTTTCGGGTG[G/A]
AAGTCCTGTGTCTAAGCGTGTGATGGTAAATGGAAAAGAATGCTTGATGTTTGTGAGAGAAGGAAAAGCACCACAAGCAAGTGAGGTGACTAATCTTGTG
Reverse complement sequence
CACAAGATTAGTCACCTCACTTGCTTGTGGTGCTTTTCCTTCTCTCACAAACATCAAGCATTCTTTTCCATTTACCATCACACGCTTAGACACAGGACTT[C/T]
CACCCGAAAACCCGAGCCCGTGTCCATCCTTGTTAGGATGAGCGGTGATGGTCTTGTAAAGGGCATCTTTTGAATGGTATGTCTTCATGCATCCATATTT
Allele Frequencies:
| 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 | 93.10% | 0.50% | 6.35% | 0.00% | NA |
| All Indica | 2759 | 88.90% | 0.80% | 10.33% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 95.20% | 0.70% | 4.09% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 70.50% | 2.80% | 26.67% | 0.00% | NA |
| Indica III | 913 | 88.90% | 0.10% | 10.95% | 0.00% | NA |
| Indica Intermediate | 786 | 91.50% | 0.90% | 7.63% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 1.10% | 4.44% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0515100790 | G -> A | LOC_Os05g26000.1 | missense_variant ; p.Gly615Glu; MODERATE | nonsynonymous_codon ; G615E | Average:39.342; most accessible tissue: Minghui63 flag leaf, score: 61.847 | possibly damaging  |
1.931 |
TOLERATED | 0.16 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0515100790 | 2.80E-06 | NA | mr1889 | 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 |