Search for Variation information by Variation ID:
Detailed information for vg0334098336:
| Variant ID: vg0334098336 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34098336 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.66, G: 0.33, others allele: 0.00, population size: 268. )
Flanking Sequence (100 bp) in Reference Genome:
CAGCTGGAGTCGTATGCAACCTACGGGTTGCGAGAGATGTACAACTCCGGTGTTGACGACATCGACGATCGTCCCACTATGGGATCTTTGTGGACACACT[G/A]
TGAGGTAAATTTTGTTTAATTCGTTTGTGTTCTCATTATGAACAGTTCCGTATTAGTTCAATACTTTCCTGATATAACTAATCATAACTATTATCTTCTT
Reverse complement sequence
AAGAAGATAATAGTTATGATTAGTTATATCAGGAAAGTATTGAACTAATACGGAACTGTTCATAATGAGAACACAAACGAATTAAACAAAATTTACCTCA[C/T]
AGTGTGTCCACAAAGATCCCATAGTGGGACGATCGTCGATGTCGTCAACACCGGAGTTGTACATCTCTCGCAACCCGTAGGTTGCATACGACTCCAGCTG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 53.40% | 45.90% | 0.13% | 0.55% | NA |
| All Indica | 2759 | 81.00% | 18.00% | 0.18% | 0.76% | NA |
| All Japonica | 1512 | 2.10% | 97.80% | 0.07% | 0.07% | NA |
| Aus | 269 | 79.90% | 20.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 86.90% | 12.60% | 0.00% | 0.50% | NA |
| Indica II | 465 | 91.80% | 7.50% | 0.22% | 0.43% | NA |
| Indica III | 913 | 69.90% | 29.40% | 0.00% | 0.77% | NA |
| Indica Intermediate | 786 | 83.20% | 15.10% | 0.51% | 1.15% | NA |
| Temperate Japonica | 767 | 0.40% | 99.50% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 5.20% | 94.60% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 5.20% | 93.80% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 42.20% | 54.40% | 0.00% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334098336 | G -> A | LOC_Os03g59910.1 | missense_variant ; p.Cys22Tyr; MODERATE | nonsynonymous_codon ; C22Y | Average:49.069; most accessible tissue: Minghui63 panicle, score: 59.629 | benign  |
-0.925 |
TOLERATED | 0.06 |
| vg0334098336 | G -> DEL | LOC_Os03g59910.1 | N | frameshift_variant | Average:49.069; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0334098336 | NA | 1.43E-09 | mr1249 | 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 |
| vg0334098336 | NA | 1.03E-08 | mr1198_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 |
| vg0334098336 | NA | 3.62E-14 | mr1579_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 |