Search for Variation information by Variation ID:
Detailed information for vg0523266234:
| Variant ID: vg0523266234 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 23266234 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.57, A: 0.43, others allele: 0.00, population size: 76. )
Flanking Sequence (100 bp) in Reference Genome:
TTGATGAAGGCCTGCCGCTCCGGGGCTTGACGCCGCACCTTCTGCCGGACAGGTCGCGCATCCGGCCGCACGGCAAGGCGGTGCTCGATCACCTCCCTGG[A/G]
GACCCCGGGCATATCCGACGGCTTCCATGCGAAAACGTCAGAATTTGCCCGCAGGAAGAAGACGAGCGCGCCTTCCTATTTGGCGTCCAAGGTTCCGCCA
Reverse complement sequence
TGGCGGAACCTTGGACGCCAAATAGGAAGGCGCGCTCGTCTTCTTCCTGCGGGCAAATTCTGACGTTTTCGCATGGAAGCCGTCGGATATGCCCGGGGTC[T/C]
CCAGGGAGGTGATCGAGCACCGCCTTGCCGTGCGGCCGGATGCGCGACCTGTCCGGCAGAAGGTGCGGCGTCAAGCCCCGGAGCGGCAGGCCTTCATCAA
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 | 60.30% | 38.60% | 1.06% | 0.00% | NA |
| All Indica | 2759 | 90.80% | 8.40% | 0.80% | 0.00% | NA |
| All Japonica | 1512 | 1.60% | 98.40% | 0.00% | 0.00% | NA |
| Aus | 269 | 91.40% | 4.10% | 4.46% | 0.00% | NA |
| Indica I | 595 | 92.40% | 5.90% | 1.68% | 0.00% | NA |
| Indica II | 465 | 93.30% | 6.00% | 0.65% | 0.00% | NA |
| Indica III | 913 | 87.80% | 11.70% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 91.30% | 8.00% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 0.70% | 99.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 2.00% | 98.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 3.70% | 96.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 29.20% | 58.30% | 12.50% | 0.00% | NA |
| Intermediate | 90 | 55.60% | 40.00% | 4.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0523266234 | A -> G | LOC_Os05g39620.1 | missense_variant ; p.Ser511Pro; MODERATE | nonsynonymous_codon ; S511P | Average:58.602; most accessible tissue: Zhenshan97 flag leaf, score: 80.799 | benign  |
-1.133 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0523266234 | NA | 5.09E-06 | mr1336 | Ind_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 |
| vg0523266234 | 5.98E-07 | NA | mr1591 | 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 |
| vg0523266234 | 2.85E-07 | NA | mr1594 | 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 |
| vg0523266234 | NA | 6.14E-35 | mr1828 | 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 |
| vg0523266234 | NA | 2.79E-10 | mr1905 | 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 |