Search for Variation information by Variation ID:
Detailed information for vg1118012029:
| Variant ID: vg1118012029 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 18012029 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCTTGAACCGTCTCAAAAGATCCTTCGTGTACTTCGTTTGATGCACAAAAGTACCTTGAGGTGTTTGCTTAATTTGCAACCCAAAAAGTACGATAACTCA[C/T]
CCATCATGCTCATCTCAAATTCCCTGCGCATAGTCTCAGTAAAATCTACAACCAAAGCGTGAGTCGAACAACCAAAGATGATATCATCCACATAAATCTG
Reverse complement sequence
CAGATTTATGTGGATGATATCATCTTTGGTTGTTCGACTCACGCTTTGGTTGTAGATTTTACTGAGACTATGCGCAGGGAATTTGAGATGAGCATGATGG[G/A]
TGAGTTATCGTACTTTTTGGGTTGCAAATTAAGCAAACACCTCAAGGTACTTTTGTGCATCAAACGAAGTACACGAAGGATCTTTTGAGACGGTTCAAGA
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 | 88.30% | 7.20% | 2.05% | 2.45% | NA |
| All Indica | 2759 | 81.60% | 12.30% | 2.79% | 3.33% | NA |
| All Japonica | 1512 | 99.50% | 0.10% | 0.20% | 0.20% | NA |
| Aus | 269 | 94.80% | 0.00% | 2.60% | 2.60% | NA |
| Indica I | 595 | 46.40% | 39.80% | 5.71% | 8.07% | NA |
| Indica II | 465 | 95.50% | 2.60% | 1.72% | 0.22% | NA |
| Indica III | 913 | 95.20% | 0.30% | 1.97% | 2.52% | NA |
| Indica Intermediate | 786 | 84.40% | 10.90% | 2.16% | 2.54% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.40% | 0.41% | 1.24% | NA |
| VI/Aromatic | 96 | 78.10% | 0.00% | 10.42% | 11.46% | NA |
| Intermediate | 90 | 93.30% | 3.30% | 0.00% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1118012029 | C -> T | LOC_Os11g30960.1 | missense_variant ; p.Gly915Asp; MODERATE | nonsynonymous_codon ; G915D | Average:15.287; most accessible tissue: Zhenshan97 flower, score: 19.041 | benign  |
0.867 |
DELETERIOUS | 0.00 |
| vg1118012029 | C -> DEL | LOC_Os11g30960.1 | N | frameshift_variant | Average:15.287; most accessible tissue: Zhenshan97 flower, score: 19.041 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1118012029 | NA | 8.41E-06 | mr1217 | 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 |
| vg1118012029 | NA | 4.14E-07 | mr1272 | 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 |
| vg1118012029 | 3.92E-06 | 3.92E-06 | mr1845 | 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 |