Search for Variation information by Variation ID:
Detailed information for vg0327526492:
| Variant ID: vg0327526492 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 27526492 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 232. )
Flanking Sequence (100 bp) in Reference Genome:
CTCGATTTCTTTGTGGGCAGACCTGTGGCAGCAGTTCATCGCCAATTTCCAAGGAACTTACAAGCGCCACGCGATTGAAGATGACCTACATGCGTTGACA[C/T]
ATAACTCGGGTGAATCCCTACGGGAATTTGTTCGGCGCTTTAACGAGTGCAGGAATACAATCCCTGAGATCACCGACGCTTCTGTAATTCGCGCCTTTAA
Reverse complement sequence
TTAAAGGCGCGAATTACAGAAGCGTCGGTGATCTCAGGGATTGTATTCCTGCACTCGTTAAAGCGCCGAACAAATTCCCGTAGGGATTCACCCGAGTTAT[G/A]
TGTCAACGCATGTAGGTCATCTTCAATCGCGTGGCGCTTGTAAGTTCCTTGGAAATTGGCGATGAACTGCTGCCACAGGTCTGCCCACAAAGAAATCGAG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.00% | 12.10% | 3.83% | 2.07% | NA |
| All Indica | 2759 | 71.80% | 18.30% | 6.45% | 3.52% | NA |
| All Japonica | 1512 | 99.60% | 0.30% | 0.07% | 0.00% | NA |
| Aus | 269 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 54.60% | 25.70% | 7.39% | 12.27% | NA |
| Indica II | 465 | 57.40% | 29.50% | 11.18% | 1.94% | NA |
| Indica III | 913 | 90.60% | 6.40% | 2.85% | 0.22% | NA |
| Indica Intermediate | 786 | 71.40% | 19.80% | 7.12% | 1.65% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 53.10% | 46.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 15.60% | 2.22% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0327526492 | C -> T | LOC_Os03g48330.1 | missense_variant ; p.His624Tyr; MODERATE | stop_gained | Average:44.065; most accessible tissue: Minghui63 young leaf, score: 61.007 | N | N | N | N |
| vg0327526492 | C -> T | LOC_Os03g48330.1 | missense_variant ; p.His624Tyr; MODERATE | nonsynonymous_codon ; H624Y | Average:44.065; most accessible tissue: Minghui63 young leaf, score: 61.007 | benign  |
1.26 |
DELETERIOUS | 0.00 |
| vg0327526492 | C -> DEL | LOC_Os03g48330.1 | N | frameshift_variant | Average:44.065; most accessible tissue: Minghui63 young leaf, score: 61.007 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0327526492 | 8.67E-06 | NA | mr1409_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 |
| vg0327526492 | 5.08E-07 | NA | mr1649_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 |
| vg0327526492 | 3.65E-06 | NA | mr1649_2 | Ind_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 |