Search for Variation information by Variation ID:
Detailed information for vg0625030338:
| Variant ID: vg0625030338 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 25030338 |
| 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: 272. )
Flanking Sequence (100 bp) in Reference Genome:
GTATTTTCTTCGGAGTGTCAGGTTCGGAGCATTAACCTTTGGTTTGGAAGGAGCATTGCCACCTGCTGTATTCTGATAAGCATGCATATTCCGAAAGAGT[G/A]
GTGGTGGAGCAATGCCAGAAGCCTGCAAAAATTAAATTAATTAAATAGAAAATTGTGATAGCGCAACCATAGATCACATGTCTTTACACTGTATTGTGAT
Reverse complement sequence
ATCACAATACAGTGTAAAGACATGTGATCTATGGTTGCGCTATCACAATTTTCTATTTAATTAATTTAATTTTTGCAGGCTTCTGGCATTGCTCCACCAC[C/T]
ACTCTTTCGGAATATGCATGCTTATCAGAATACAGCAGGTGGCAATGCTCCTTCCAAACCAAAGGTTAATGCTCCGAACCTGACACTCCGAAGAAAATAC
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 | 84.30% | 15.70% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 65.10% | 34.80% | 0.07% | 0.00% | NA |
| Aus | 269 | 91.40% | 8.20% | 0.37% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 95.50% | 4.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 92.40% | 7.60% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 91.00% | 8.90% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 34.50% | 65.50% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 46.90% | 53.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 20.80% | 79.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 67.80% | 32.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0625030338 | G -> A | LOC_Os06g41750.1 | missense_variant ; p.Pro251Leu; MODERATE | nonsynonymous_codon ; P251L | Average:52.128; most accessible tissue: Minghui63 flag leaf, score: 76.091 | possibly damaging  |
1.728 |
TOLERATED | 0.12 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0625030338 | NA | 2.97E-07 | mr1057_2 | 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 |
| vg0625030338 | NA | 9.70E-09 | mr1449_2 | 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 |
| vg0625030338 | NA | 4.95E-12 | mr1533_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 |
| vg0625030338 | NA | 2.61E-06 | mr1606_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 |
| vg0625030338 | NA | 2.77E-06 | mr1873_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 |
| vg0625030338 | NA | 1.81E-09 | mr1980_2 | 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 |