Search for Variation information by Variation ID:
Detailed information for vg1106255697:
| Variant ID: vg1106255697 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 6255697 |
| 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: 331. )
Flanking Sequence (100 bp) in Reference Genome:
GGAGCCGCTCCTTGTTCCTTGCCGTTATCCCTGACAAGGACGTATGACTTAGGAGACGAAGTTTTCATGGCGCCGAGGAGGACTTTGCAACTCAAGAGGT[C/T]
GTGATTCTTTGTCTTGTGAATAGGACAATAGACATCTCGAGTTAGAGAAGTACGCTGAATTCCACGTTCTTTGCAGGCGCGAATTTCAACGTGGACGTTG
Reverse complement sequence
CAACGTCCACGTTGAAATTCGCGCCTGCAAAGAACGTGGAATTCAGCGTACTTCTCTAACTCGAGATGTCTATTGTCCTATTCACAAGACAAAGAATCAC[G/A]
ACCTCTTGAGTTGCAAAGTCCTCCTCGGCGCCATGAAAACTTCGTCTCCTAAGTCATACGTCCTTGTCAGGGATAACGGCAAGGAACAAGGAGCGGCTCC
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 | 96.10% | 3.20% | 0.61% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 90.50% | 8.10% | 1.39% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 94.10% | 4.30% | 1.56% | 0.00% | NA |
| Tropical Japonica | 504 | 96.60% | 3.00% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 66.40% | 30.70% | 2.90% | 0.00% | NA |
| VI/Aromatic | 96 | 69.80% | 26.00% | 4.17% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 3.30% | 4.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1106255697 | C -> T | LOC_Os11g11290.1 | missense_variant ; p.Asp203Asn; MODERATE | nonsynonymous_codon ; D203N | Average:54.216; most accessible tissue: Minghui63 panicle, score: 66.554 | benign  |
0.407 |
TOLERATED | 0.10 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1106255697 | NA | 9.23E-06 | mr1180 | 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 |
| vg1106255697 | NA | 9.24E-06 | mr1622 | 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 |
| vg1106255697 | 1.28E-06 | 1.28E-06 | mr1197_2 | Jap_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 |
| vg1106255697 | 3.03E-06 | NA | mr1705_2 | 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 |
| vg1106255697 | NA | 9.23E-07 | mr1705_2 | 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 |