Search for Variation information by Variation ID:
Detailed information for vg0708450949:
| Variant ID: vg0708450949 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 8450949 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCTGGCGAAGAGAAGGTTGATTGAGCTGCCACCGTCGATGAGAACCCGCGCGACCTTGATGTTCCGAATAGTGGATTCGACCATGATCGGATAGCATCCT[G/A]
GGATGATGGCAGTCTTGGGATGGTCTTCTTCCGAAAATTCTATCTTCTGTTCAGACCACTTCATCTTGGGTGCAGCCCCCTGCCATGTCAAACAGACTTC
Reverse complement sequence
GAAGTCTGTTTGACATGGCAGGGGGCTGCACCCAAGATGAAGTGGTCTGAACAGAAGATAGAATTTTCGGAAGAAGACCATCCCAAGACTGCCATCATCC[C/T]
AGGATGCTATCCGATCATGGTCGAATCCACTATTCGGAACATCAAGGTCGCGCGGGTTCTCATCGACGGTGGCAGCTCAATCAACCTTCTCTTCGCCAGC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.90% | 2.90% | 1.18% | 0.00% | NA |
| All Indica | 2759 | 98.90% | 0.00% | 1.05% | 0.00% | NA |
| All Japonica | 1512 | 89.40% | 8.90% | 1.72% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 96.80% | 0.00% | 3.18% | 0.00% | NA |
| Temperate Japonica | 767 | 93.70% | 3.80% | 2.48% | 0.00% | NA |
| Tropical Japonica | 504 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 62.20% | 34.90% | 2.90% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 2.20% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0708450949 | G -> A | LOC_Os07g14800.1 | missense_variant ; p.Pro740Leu; MODERATE | nonsynonymous_codon ; P740L | Average:43.641; most accessible tissue: Minghui63 panicle, score: 62.157 | benign  |
0.428 |
TOLERATED | 0.07 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0708450949 | 3.00E-08 | 1.66E-07 | mr1038_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 |
| vg0708450949 | 4.52E-09 | 4.52E-09 | mr1389_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 |