Search for Variation information by Variation ID:
Detailed information for vg0627868980:
| Variant ID: vg0627868980 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 27868980 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 327. )
Flanking Sequence (100 bp) in Reference Genome:
TTTTTGCACATGGGTGTTCTACAAAACAATCACATTTTGGCAGCTTGTAACATACTTCTCAGAGAGAATGATATCGCCAGAAACACTTCGGAGAAACAGC[G/A]
TAATGCAGCGTAACTGGAGTAATAAGGTATAGATGGATGCATTTCCGTAGATCTGCTTTGGATACAACATCTTTGTGTTAGCATTGTAAGTACATTTTGT
Reverse complement sequence
ACAAAATGTACTTACAATGCTAACACAAAGATGTTGTATCCAAAGCAGATCTACGGAAATGCATCCATCTATACCTTATTACTCCAGTTACGCTGCATTA[C/T]
GCTGTTTCTCCGAAGTGTTTCTGGCGATATCATTCTCTCTGAGAAGTATGTTACAAGCTGCCAAAATGTGATTGTTTTGTAGAACACCCATGTGCAAAAA
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 | 98.70% | 0.90% | 0.44% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 96.10% | 2.70% | 1.19% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.10% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 92.70% | 5.20% | 2.09% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0627868980 | G -> A | LOC_Os06g45980.1 | missense_variant ; p.Val234Ile; MODERATE | nonsynonymous_codon ; V234I | Average:41.007; most accessible tissue: Callus, score: 71.646 | benign  |
1.092 |
TOLERATED | 0.14 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0627868980 | NA | 6.27E-06 | mr1028 | 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 |
| vg0627868980 | NA | 6.31E-06 | mr1245 | 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 |
| vg0627868980 | 1.98E-07 | 1.98E-07 | mr1369 | Jap_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 |
| vg0627868980 | NA | 4.25E-06 | mr1453 | 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 |
| vg0627868980 | NA | 2.26E-07 | mr1652 | 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 |
| vg0627868980 | NA | 7.62E-06 | mr1921 | 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 |
| vg0627868980 | NA | 1.80E-06 | mr1164_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 |