Search for Variation information by Variation ID:
Detailed information for vg0921847328:
| Variant ID: vg0921847328 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 21847328 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 291. )
Flanking Sequence (100 bp) in Reference Genome:
TATGTTCCAACAACACGCCGGGTATTTGCATTTTGTTGATTATCACAAAAGATCCTTGCCATACCAAAATCTGCTATCTTGGGTCTCATCTCTGCATCCA[T/G]
TAAAACGTTGCTGGCTTTGAGATCTCTATGAATTATGGTTAATCTTGAATCTTGGTGCAGATAAAGAAGTCCCCTAGCTACTCCTTTGATTATATTAAAC
Reverse complement sequence
GTTTAATATAATCAAAGGAGTAGCTAGGGGACTTCTTTATCTGCACCAAGATTCAAGATTAACCATAATTCATAGAGATCTCAAAGCCAGCAACGTTTTA[A/C]
TGGATGCAGAGATGAGACCCAAGATAGCAGATTTTGGTATGGCAAGGATCTTTTGTGATAATCAACAAAATGCAAATACCCGGCGTGTTGTTGGAACATA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.00% | 7.40% | 1.65% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.20% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 72.70% | 22.30% | 5.03% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.60% | 0.22% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 56.80% | 35.70% | 7.43% | 0.00% | NA |
| Tropical Japonica | 504 | 94.20% | 3.80% | 1.98% | 0.00% | NA |
| Japonica Intermediate | 241 | 78.00% | 18.30% | 3.73% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0921847328 | T -> G | LOC_Os09g37890.1 | missense_variant ; p.Met590Leu; MODERATE | nonsynonymous_codon ; M590L | Average:23.41; most accessible tissue: Callus, score: 38.337 | probably damaging  |
-2.583 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0921847328 | 2.21E-07 | 1.05E-09 | mr1530 | 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 |
| vg0921847328 | NA | 7.22E-08 | mr1530 | 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 |
| vg0921847328 | NA | 1.74E-06 | mr1880 | 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 |
| vg0921847328 | 5.22E-06 | NA | mr1530_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 |
| vg0921847328 | NA | 5.32E-11 | mr1530_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 |