Search for Variation information by Variation ID:
Detailed information for vg0501033512:
| Variant ID: vg0501033512 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 1033512 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AAGTATAGGAGCAAGTCTAGCGTTGGCAATGACCAAATCTCTTTATCCGAGGGTTGACGTTGATGCCATTGATGGCTTTGCAGATGGGACGAGCGAAGAA[G/T]
CTGCTCTTGACCTCATCAGCGATGCGCAGAAAGCCACTGACAAGATTGCTGCTGATGTAGTTGAGAGATTCTAGGACACCGATCATCGACCGACTGGTCC
Reverse complement sequence
GGACCAGTCGGTCGATGATCGGTGTCCTAGAATCTCTCAACTACATCAGCAGCAATCTTGTCAGTGGCTTTCTGCGCATCGCTGATGAGGTCAAGAGCAG[C/A]
TTCTTCGCTCGTCCCATCTGCAAAGCCATCAATGGCATCAACGTCAACCCTCGGATAAAGAGATTTGGTCATTGCCAACGCTAGACTTGCTCCTATACTT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.00% | 3.90% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 87.50% | 12.20% | 0.33% | 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 | 89.00% | 10.30% | 0.65% | 0.00% | NA |
| Tropical Japonica | 504 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 61.80% | 38.20% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0501033512 | G -> T | LOC_Os05g02850.1 | missense_variant ; p.Ala644Ser; MODERATE | nonsynonymous_codon ; A644S | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
1.465 |
DELETERIOUS | 0.04 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0501033512 | 5.48E-07 | NA | mr1613_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 |