Search for Variation information by Variation ID:
Detailed information for vg0138239162:
| Variant ID: vg0138239162 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 38239162 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGCAAGCGGGCTGGACGGCGCCGGCGGCGTGCACCTCCACCACCGAGACGACGCCGGTTGTCTATCGCGGATGAACTCGTCCATGAGGTCCAGCTTCTTC[T/C]
GCGCGACGCGCTCGACCTCGGGGATTTCGGACGGGCGGCAGATCGTGGCGGATCTGCACCACGAGTAGAACTCGTCGAGCTCGTCGAACAGCTTGGCGAT
Reverse complement sequence
ATCGCCAAGCTGTTCGACGAGCTCGACGAGTTCTACTCGTGGTGCAGATCCGCCACGATCTGCCGCCCGTCCGAAATCCCCGAGGTCGAGCGCGTCGCGC[A/G]
GAAGAAGCTGGACCTCATGGACGAGTTCATCCGCGATAGACAACCGGCGTCGTCTCGGTGGTGGAGGTGCACGCCGCCGGCGCCGTCCAGCCCGCTTGCC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.70% | 3.40% | 0.83% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 86.70% | 10.70% | 2.58% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 82.00% | 13.30% | 4.69% | 0.00% | NA |
| Tropical Japonica | 504 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 78.40% | 20.30% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0138239162 | T -> C | LOC_Os01g65860.1 | missense_variant ; p.Gln324Arg; MODERATE | nonsynonymous_codon ; Q324R | Average:79.887; most accessible tissue: Zhenshan97 flag leaf, score: 86.342 | possibly damaging  |
1.504 |
TOLERATED | 0.18 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0138239162 | 9.54E-07 | 5.15E-07 | mr1070 | 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 |
| vg0138239162 | 4.79E-06 | 2.22E-06 | mr1097 | 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 |
| vg0138239162 | 1.92E-06 | 2.11E-06 | mr1154 | 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 |