Search for Variation information by Variation ID:
Detailed information for vg1019364275:
| Variant ID: vg1019364275 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 19364275 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GACGGCGGCGCCGGAGGATCCTCCTCCTCCTCCTACTCGGATGTCTGGGTGCGTGATCGGGGTTCGGCGTGGTGGGACGGTGGATGTCTCCGACATCTTG[G/C]
ACATCTTGATCTTGCACGGCCCCGACCCCGCAACCTTCGACCGCGCCTTACTGGAGAAGGATCAGGAGATCTGTAACTAAAGCTGCTAGCTACCCCCAAG
Reverse complement sequence
CTTGGGGGTAGCTAGCAGCTTTAGTTACAGATCTCCTGATCCTTCTCCAGTAAGGCGCGGTCGAAGGTTGCGGGGTCGGGGCCGTGCAAGATCAAGATGT[C/G]
CAAGATGTCGGAGACATCCACCGTCCCACCACGCCGAACCCCGATCACGCACCCAGACATCCGAGTAGGAGGAGGAGGAGGATCCTCCGGCGCCGCCGTC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.70% | 2.60% | 0.68% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 89.90% | 7.90% | 2.12% | 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 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 96.10% | 2.10% | 1.83% | 0.00% | NA |
| Tropical Japonica | 504 | 95.60% | 4.00% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 58.50% | 34.90% | 6.64% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1019364275 | G -> C | LOC_Os10g36229.1 | missense_variant ; p.Asp90His; MODERATE | nonsynonymous_codon ; D90H | Average:50.311; most accessible tissue: Zhenshan97 young leaf, score: 77.422 | probably damaging  |
2.873 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1019364275 | 1.83E-06 | 1.57E-09 | mr1691 | 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 |
| vg1019364275 | NA | 3.56E-08 | mr1693 | 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 |