Search for Variation information by Variation ID:
Detailed information for vg0219768664:
| Variant ID: vg0219768664 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 19768664 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 127. )
Flanking Sequence (100 bp) in Reference Genome:
AAATCAGACCCTCCAACTGCTCAACGCCGATCACCCCATCGGCAAACTGGTCAAGCTGGCGGAGGACCTAAAATCCGGTCTGATTCTCAACCCAGCACCA[C/T]
TCAATCGGCCAACCAATCAGACTTCCGCAAGAGGAAATTGGTTATGAGCGACGATGAAAATGATGACTCTGAAAAAGCTGGCAGCAAGGGGGTGACTTGA
Reverse complement sequence
TCAAGTCACCCCCTTGCTGCCAGCTTTTTCAGAGTCATCATTTTCATCGTCGCTCATAACCAATTTCCTCTTGCGGAAGTCTGATTGGTTGGCCGATTGA[G/A]
TGGTGCTGGGTTGAGAATCAGACCGGATTTTAGGTCCTCCGCCAGCTTGACCAGTTTGCCGATGGGGTGATCGGCGTTGAGCAGTTGGAGGGTCTGATTT
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 | 95.10% | 3.90% | 1.02% | 0.00% | NA |
| All Indica | 2759 | 91.80% | 6.50% | 1.70% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.80% | 0.50% | 1.68% | 0.00% | NA |
| Indica II | 465 | 77.20% | 17.80% | 4.95% | 0.00% | NA |
| Indica III | 913 | 96.20% | 3.60% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 90.80% | 7.60% | 1.53% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | 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 | 96.70% | 2.20% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0219768664 | C -> T | LOC_Os02g33260.1 | missense_variant ; p.Thr202Ile; MODERATE | nonsynonymous_codon ; T202I | Average:49.972; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 | possibly damaging  |
1.822 |
DELETERIOUS | 0.03 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0219768664 | NA | 7.10E-06 | mr1149 | 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 |
| vg0219768664 | NA | 5.53E-07 | mr1897_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 |
| vg0219768664 | 4.35E-06 | 1.85E-08 | mr1914_2 | 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 |
| vg0219768664 | NA | 1.87E-06 | mr1927_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 |