Search for Variation information by Variation ID:
Detailed information for vg0117820821:
| Variant ID: vg0117820821 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 17820821 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.60, T: 0.40, others allele: 0.00, population size: 100. )
Flanking Sequence (100 bp) in Reference Genome:
TACAAGCCGAGATCCGTGCCTGCAAAGAGCGTGGAATTCAACATACTTCTCCAACCCATGATGTCTATTGTCCTATTCATAAGACAAAGAATCACGACTT[C/T]
TCAAGCTGCAAGGTTCTTCTCAGCGCCATGAGGACGCCACCTCCTAAGGTCCAGCAGTCACAAATCTCTTCTAGAGATACGGACAAGGAACGAGGAGCGA
Reverse complement sequence
TCGCTCCTCGTTCCTTGTCCGTATCTCTAGAAGAGATTTGTGACTGCTGGACCTTAGGAGGTGGCGTCCTCATGGCGCTGAGAAGAACCTTGCAGCTTGA[G/A]
AAGTCGTGATTCTTTGTCTTATGAATAGGACAATAGACATCATGGGTTGGAGAAGTATGTTGAATTCCACGCTCTTTGCAGGCACGGATCTCGGCTTGTA
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 | 49.60% | 40.60% | 5.33% | 4.44% | NA |
| All Indica | 2759 | 75.60% | 8.00% | 8.95% | 7.36% | NA |
| All Japonica | 1512 | 2.30% | 97.50% | 0.00% | 0.20% | NA |
| Aus | 269 | 68.80% | 31.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 51.40% | 4.40% | 24.37% | 19.83% | NA |
| Indica II | 465 | 67.50% | 21.10% | 5.16% | 6.24% | NA |
| Indica III | 913 | 96.20% | 1.00% | 1.64% | 1.20% | NA |
| Indica Intermediate | 786 | 74.90% | 11.30% | 8.02% | 5.73% | NA |
| Temperate Japonica | 767 | 0.90% | 99.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 5.00% | 94.60% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 1.20% | 98.30% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 6.20% | 93.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 33.30% | 56.70% | 5.56% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0117820821 | C -> T | LOC_Os01g32500.1 | synonymous_variant ; p.Phe150Phe; LOW | synonymous_codon | Average:60.698; most accessible tissue: Minghui63 flag leaf, score: 79.085 | N | N | N | N |
| vg0117820821 | C -> T | LOC_Os01g32500.1 | synonymous_variant ; p.Phe150Phe; LOW | nonsynonymous_codon ; F150H | Average:60.698; most accessible tissue: Minghui63 flag leaf, score: 79.085 | probably damaging  |
2.434 |
DELETERIOUS | 0.00 |
| vg0117820821 | C -> T | LOC_Os01g32500.1 | synonymous_variant ; p.Phe150Phe; LOW | nonsynonymous_codon ; F150L | Average:60.698; most accessible tissue: Minghui63 flag leaf, score: 79.085 | benign |
-0.744 |
TOLERATED | 1.00 |
| vg0117820821 | C -> DEL | LOC_Os01g32500.1 | N | frameshift_variant | Average:60.698; most accessible tissue: Minghui63 flag leaf, score: 79.085 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0117820821 | 4.07E-06 | NA | mr1312 | 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 |