Search for Variation information by Variation ID:
Detailed information for vg0230185057:
| Variant ID: vg0230185057 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 30185057 |
| Reference Allele: A | Alternative Allele: G |
| 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: 123. )
Flanking Sequence (100 bp) in Reference Genome:
CTAGCTATGCATGAAGAGGAAGTACATAATAATGCCGATTATTATTCAAGGCCCCAAGCAACCTGGTAATGACATCGATGTGTACCTAAGACCACTGGTC[A/G]
AAGATCTTAAACTGTTGTGGAAAAAGGAAGGTGTCCCCATGTGGGACGAGGACAAACAGGAGGAGTTTAACCTACGAGCGTTGCTGTTCGTAACCATCAA
Reverse complement sequence
TTGATGGTTACGAACAGCAACGCTCGTAGGTTAAACTCCTCCTGTTTGTCCTCGTCCCACATGGGGACACCTTCCTTTTTCCACAACAGTTTAAGATCTT[T/C]
GACCAGTGGTCTTAGGTACACATCGATGTCATTACCAGGTTGCTTGGGGCCTTGAATAATAATCGGCATTATTATGTACTTCCTCTTCATGCATAGCTAG
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 | 49.00% | 42.10% | 8.95% | 0.00% | NA |
| All Indica | 2759 | 78.50% | 10.10% | 11.38% | 0.00% | NA |
| All Japonica | 1512 | 0.70% | 99.10% | 0.20% | 0.00% | NA |
| Aus | 269 | 42.00% | 19.70% | 38.29% | 0.00% | NA |
| Indica I | 595 | 83.90% | 4.20% | 11.93% | 0.00% | NA |
| Indica II | 465 | 82.80% | 8.20% | 9.03% | 0.00% | NA |
| Indica III | 913 | 71.70% | 14.80% | 13.47% | 0.00% | NA |
| Indica Intermediate | 786 | 79.60% | 10.40% | 9.92% | 0.00% | NA |
| Temperate Japonica | 767 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.00% | 98.60% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.80% | 98.80% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 27.80% | 68.90% | 3.33% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0230185057 | A -> G | LOC_Os02g49400.1 | missense_variant ; p.Lys332Glu; MODERATE | nonsynonymous_codon ; K332E | Average:26.416; most accessible tissue: Minghui63 young leaf, score: 48.378 | benign  |
-0.72 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0230185057 | NA | 6.95E-11 | mr1175 | 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 |