Search for Variation information by Variation ID:
Detailed information for vg0608258762:
| Variant ID: vg0608258762 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 8258762 |
| Reference Allele: G | Alternative Allele: T,A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCAGAGGCAAGCATCGCCAAGGGGTATGGAATAGAGGAGGTCATCGAATTTTGCATAGAATTTATAGAAGACCTTCGCCCAATCGGGGTACCTGAATCAC[G/T,A]
CCATGAAGGGAGACTACGGGGAAAGGGAACTCTCGGAAGGAAAGCAATAATGACGGTAGACAACAATTTATTCCGTAAAGCCCATTTCACGGTTCTGCAA
Reverse complement sequence
TTGCAGAACCGTGAAATGGGCTTTACGGAATAAATTGTTGTCTACCGTCATTATTGCTTTCCTTCCGAGAGTTCCCTTTCCCCGTAGTCTCCCTTCATGG[C/A,T]
GTGATTCAGGTACCCCGATTGGGCGAAGGTCTTCTATAAATTCTATGCAAAATTCGATGACCTCCTCTATTCCATACCCCTTGGCGATGCTTGCCTCTGG
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 | 97.90% | 0.80% | 0.74% | 0.00% | T: 0.51% |
| All Indica | 2759 | 99.30% | 0.00% | 0.07% | 0.00% | T: 0.62% |
| All Japonica | 1512 | 95.20% | 2.60% | 2.12% | 0.00% | NA |
| Aus | 269 | 97.00% | 0.00% | 0.37% | 0.00% | T: 2.60% |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.90% | 0.00% | 0.22% | 0.00% | T: 1.86% |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 90.60% | 5.20% | 4.17% | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0608258762 | G -> T | LOC_Os06g14680.1 | missense_variant ; p.Arg575Leu; MODERATE | nonsynonymous_codon ; R575L | Average:21.963; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 | benign  |
0.63 |
DELETERIOUS | 0.01 |
| vg0608258762 | G -> A | LOC_Os06g14680.1 | missense_variant ; p.Arg575His; MODERATE | nonsynonymous_codon ; R575H | Average:21.963; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 | benign |
1.055 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0608258762 | 6.06E-06 | 1.76E-07 | mr1305_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 |
| vg0608258762 | 4.15E-06 | 3.80E-07 | mr1409_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 |
| vg0608258762 | 4.48E-06 | 4.48E-06 | mr1445_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 |
| vg0608258762 | 4.66E-06 | 9.51E-09 | mr1585_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 |
| vg0608258762 | 9.03E-06 | 9.03E-06 | mr1647_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 |
| vg0608258762 | NA | 3.57E-06 | mr1765_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 |