Search for Variation information by Variation ID:
Detailed information for vg0210660828:
| Variant ID: vg0210660828 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 10660828 |
| 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: 241. )
Flanking Sequence (100 bp) in Reference Genome:
GACTTGTTTGATCAGCTTAAAGATGCCACCGTTTTCTCCAAGATCGATCTTCGATCAAGGTATCACCAGTTGAGGATCAAAGAGGAAGATATACCTAAGA[C/T]
GGCTTTTACCACTCGGTATGGGTTGTTTGAATGTACTGTTATGTCTGTTGGACTTACCAATGCCCCCGCTTTCTTCATGAACTTGATGAATAAGGTGTTT
Reverse complement sequence
AAACACCTTATTCATCAAGTTCATGAAGAAAGCGGGGGCATTGGTAAGTCCAACAGACATAACAGTACATTCAAACAACCCATACCGAGTGGTAAAAGCC[G/A]
TCTTAGGTATATCTTCCTCTTTGATCCTCAACTGGTGATACCTTGATCGAAGATCGATCTTGGAGAAAACGGTGGCATCTTTAAGCTGATCAAACAAGTC
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 | 93.40% | 4.60% | 1.97% | 0.00% | NA |
| All Indica | 2759 | 99.30% | 0.20% | 0.54% | 0.00% | NA |
| All Japonica | 1512 | 81.70% | 13.80% | 4.50% | 0.00% | NA |
| Aus | 269 | 96.70% | 0.40% | 2.97% | 0.00% | NA |
| Indica I | 595 | 98.70% | 0.00% | 1.34% | 0.00% | NA |
| Indica II | 465 | 98.90% | 0.20% | 0.86% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.40% | 0.30% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 66.10% | 26.30% | 7.56% | 0.00% | NA |
| Tropical Japonica | 504 | 98.60% | 0.00% | 1.39% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.90% | 2.90% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0210660828 | C -> T | LOC_Os02g18340.1 | missense_variant ; p.Thr772Met; MODERATE | nonsynonymous_codon ; T772M | Average:37.605; most accessible tissue: Minghui63 flag leaf, score: 59.912 | probably damaging  |
2.645 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0210660828 | 7.96E-07 | NA | mr1300 | 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 |
| vg0210660828 | 4.67E-09 | NA | mr1310 | 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 |
| vg0210660828 | NA | 9.83E-08 | mr1310 | Jap_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 |
| vg0210660828 | NA | 9.11E-10 | mr1712 | 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 |
| vg0210660828 | 7.71E-10 | NA | mr1926 | 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 |
| vg0210660828 | NA | 5.72E-08 | mr1926 | Jap_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 |
| vg0210660828 | NA | 3.06E-09 | mr1959 | 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 |