Search for Variation information by Variation ID:
Detailed information for vg0209673998:
| Variant ID: vg0209673998 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9673998 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 236. )
Flanking Sequence (100 bp) in Reference Genome:
GAAACTGTCTTGGGTTGTTTCCAGTTGGTTACGGATTCCACGTTACTAGGATCAACGGCAACTCCTCCTGCTGAGATGACGTGACCAAGGAACTTTACTT[C/T]
AGACAACCAGAATTCACATTTGCTAAACTTGGCATACAACTGATGTTCTCGCAGCTTCTCTAGTGCAAGGCGAAGATGTTCTTCATGCTCTTCTTTAGTT
Reverse complement sequence
AACTAAAGAAGAGCATGAAGAACATCTTCGCCTTGCACTAGAGAAGCTGCGAGAACATCAGTTGTATGCCAAGTTTAGCAAATGTGAATTCTGGTTGTCT[G/A]
AAGTAAAGTTCCTTGGTCACGTCATCTCAGCAGGAGGAGTTGCCGTTGATCCTAGTAACGTGGAATCCGTAACCAACTGGAAACAACCCAAGACAGTTTC
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 | 87.10% | 3.60% | 2.31% | 7.00% | NA |
| All Indica | 2759 | 79.90% | 6.20% | 3.48% | 10.44% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.07% | 0.13% | NA |
| Aus | 269 | 83.30% | 0.00% | 2.97% | 13.75% | NA |
| Indica I | 595 | 93.30% | 0.80% | 2.69% | 3.19% | NA |
| Indica II | 465 | 72.00% | 10.30% | 3.01% | 14.62% | NA |
| Indica III | 913 | 74.40% | 6.00% | 4.38% | 15.22% | NA |
| Indica Intermediate | 786 | 80.80% | 8.00% | 3.31% | 7.89% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | 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 | 91.10% | 0.00% | 4.44% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0209673998 | C -> T | LOC_Os02g16960.1 | missense_variant ; p.Glu579Lys; MODERATE | nonsynonymous_codon ; E579K | Average:24.796; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 | benign  |
0.986 |
DELETERIOUS | 0.01 |
| vg0209673998 | C -> DEL | LOC_Os02g16960.1 | N | frameshift_variant | Average:24.796; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0209673998 | NA | 1.16E-08 | mr1697 | 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 |
| vg0209673998 | NA | 4.98E-07 | mr1446_2 | 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 |