Search for Variation information by Variation ID:
Detailed information for vg0722037297:
| Variant ID: vg0722037297 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 22037297 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.11, others allele: 0.00, population size: 254. )
Flanking Sequence (100 bp) in Reference Genome:
CTCTTTGTCTGCGAAGAAGCTGTGCTATTATGCATCTGCGAAGTTTGACTTGATGAAACATCTGAGAAAAAATTTATGACATCAGGGCTTTCATCAAGAA[C/T]
CTTCAGTGACCTTGGAACAGGAGGCATGTTGACATCAAGGAATCCCTCTAAAATTTGGACGACCTGACCCATTGTAGGTCTGCCATTTTCATCATCTTGG
Reverse complement sequence
CCAAGATGATGAAAATGGCAGACCTACAATGGGTCAGGTCGTCCAAATTTTAGAGGGATTCCTTGATGTCAACATGCCTCCTGTTCCAAGGTCACTGAAG[G/A]
TTCTTGATGAAAGCCCTGATGTCATAAATTTTTTCTCAGATGTTTCATCAAGTCAAACTTCGCAGATGCATAATAGCACAGCTTCTTCGCAGACAAAGAG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.70% | 43.20% | 0.06% | 0.02% | NA |
| All Indica | 2759 | 86.80% | 13.10% | 0.11% | 0.04% | NA |
| All Japonica | 1512 | 6.00% | 94.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 59.90% | 40.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.00% | 1.70% | 0.34% | 0.00% | NA |
| Indica II | 465 | 78.30% | 21.30% | 0.22% | 0.22% | NA |
| Indica III | 913 | 87.10% | 12.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 83.00% | 17.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 0.30% | 99.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 13.90% | 86.10% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 7.50% | 92.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 0.00% | 100.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 41.10% | 58.90% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0722037297 | C -> DEL | LOC_Os07g36780.1 | N | frameshift_variant | Average:60.888; most accessible tissue: Callus, score: 85.836 | N | N | N | N |
| vg0722037297 | C -> T | LOC_Os07g36780.1 | missense_variant ; p.Val780Ile; MODERATE | nonsynonymous_codon ; V780I | Average:60.888; most accessible tissue: Callus, score: 85.836 | benign  |
0.142 |
TOLERATED | 0.19 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0722037297 | NA | 2.28E-07 | mr1212_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 |
| vg0722037297 | 9.03E-06 | NA | mr1241_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 |
| vg0722037297 | NA | 8.49E-24 | mr1949_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 |