Search for Variation information by Variation ID:
Detailed information for vg0605330241:
| Variant ID: vg0605330241 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 5330241 |
| 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: 368. )
Flanking Sequence (100 bp) in Reference Genome:
AGAGCATCCAGGACGAACACGAGGGAAAGGGGTGATTCCTTGGAAGATTGGGTTCAAGGAGGACATCCACACGTACAGGAGACGGATGAGGCGCAAGAGA[G/A]
ATACCGAGGCGAAGATTGCAGATCTAGAGTTCAGGGTATCGAGCTACGAGCGCAGCATGCAAGAGGAGGTGGCAAGGAAGGCTGATGAACGCATAGCCGC
Reverse complement sequence
GCGGCTATGCGTTCATCAGCCTTCCTTGCCACCTCCTCTTGCATGCTGCGCTCGTAGCTCGATACCCTGAACTCTAGATCTGCAATCTTCGCCTCGGTAT[C/T]
TCTCTTGCGCCTCATCCGTCTCCTGTACGTGTGGATGTCCTCCTTGAACCCAATCTTCCAAGGAATCACCCCTTTCCCTCGTGTTCGTCCTGGATGCTCT
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 | 90.80% | 8.00% | 1.16% | 0.00% | NA |
| All Indica | 2759 | 98.20% | 1.30% | 0.51% | 0.00% | NA |
| All Japonica | 1512 | 78.40% | 19.20% | 2.31% | 0.00% | NA |
| Aus | 269 | 84.80% | 14.10% | 1.12% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.00% | 0.84% | 0.00% | NA |
| Indica II | 465 | 98.30% | 1.30% | 0.43% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.30% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 95.70% | 3.60% | 0.76% | 0.00% | NA |
| Temperate Japonica | 767 | 97.10% | 1.70% | 1.17% | 0.00% | NA |
| Tropical Japonica | 504 | 54.00% | 42.30% | 3.77% | 0.00% | NA |
| Japonica Intermediate | 241 | 70.10% | 27.00% | 2.90% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 82.20% | 14.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0605330241 | G -> A | LOC_Os06g10370.1 | missense_variant ; p.Asp403Asn; MODERATE | nonsynonymous_codon ; D403N | Average:30.249; most accessible tissue: Minghui63 flag leaf, score: 45.195 | benign  |
0.614 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0605330241 | 6.92E-09 | 1.45E-06 | mr1201 | 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 |
| vg0605330241 | 1.21E-08 | 1.60E-08 | mr1219 | 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 |
| vg0605330241 | 5.31E-09 | 5.96E-08 | mr1274 | 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 |
| vg0605330241 | 1.15E-08 | 1.75E-07 | mr1201_2 | 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 |
| vg0605330241 | 3.98E-08 | 7.61E-09 | mr1219_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 |
| vg0605330241 | 1.49E-11 | 1.29E-08 | mr1274_2 | 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 |
| vg0605330241 | NA | 5.43E-06 | mr1786_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 |