Search for Variation information by Variation ID:
Detailed information for vg0220796750:
| Variant ID: vg0220796750 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 20796750 |
| 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, others allele: 0.00, population size: 313. )
Flanking Sequence (100 bp) in Reference Genome:
CCTAAATGTGTCCAAAATCCCACTCCTATGTGACAATGAGAGCGCCATTAAGATAGCTAATAACCCCGTCCAACATTCCCGAACCAAACACATAGATATT[C/T]
GCCATCATTTCTTGAGAGACCATTCCACAAGAGGCGACATAGATATCCAACATGTGAGAACCGACAAACAATTGGCGGATATGTTCACCAAGCCTCTAGA
Reverse complement sequence
TCTAGAGGCTTGGTGAACATATCCGCCAATTGTTTGTCGGTTCTCACATGTTGGATATCTATGTCGCCTCTTGTGGAATGGTCTCTCAAGAAATGATGGC[G/A]
AATATCTATGTGTTTGGTTCGGGAATGTTGGACGGGGTTATTAGCTATCTTAATGGCGCTCTCATTGTCACATAGGAGTGGGATTTTGGACACATTTAGG
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 | 91.70% | 6.30% | 1.69% | 0.25% | NA |
| All Indica | 2759 | 91.70% | 6.40% | 1.59% | 0.25% | NA |
| All Japonica | 1512 | 99.40% | 0.50% | 0.07% | 0.00% | NA |
| Aus | 269 | 45.40% | 40.50% | 12.27% | 1.86% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 75.50% | 19.40% | 5.16% | 0.00% | NA |
| Indica III | 913 | 93.60% | 5.00% | 0.88% | 0.44% | NA |
| Indica Intermediate | 786 | 92.90% | 5.20% | 1.53% | 0.38% | NA |
| Temperate Japonica | 767 | 99.50% | 0.40% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 4.40% | 2.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0220796750 | C -> T | LOC_Os02g34670.1 | missense_variant ; p.Arg389Cys; MODERATE | nonsynonymous_codon ; R389C | Average:24.486; most accessible tissue: Minghui63 flag leaf, score: 38.911 | benign  |
1.2 |
TOLERATED | 0.06 |
| vg0220796750 | C -> DEL | LOC_Os02g34670.1 | N | frameshift_variant | Average:24.486; most accessible tissue: Minghui63 flag leaf, score: 38.911 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0220796750 | NA | 4.16E-06 | mr1113 | 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 |
| vg0220796750 | NA | 3.12E-19 | mr1114 | 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 |
| vg0220796750 | 4.14E-06 | 1.83E-08 | mr1114 | 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 |
| vg0220796750 | NA | 6.75E-06 | mr1347 | 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 |