Search for Variation information by Variation ID:
Detailed information for vg0609173072:
| Variant ID: vg0609173072 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9173072 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATGGCCACATTGTCAGCAGAGGGAGCAGCGAACTCGCGGAGAGTCTTGCTAGCCATAGTCTTGAAAATTGGTGGCGCTGGTACGGCTGGTTTCTCTGTCG[G/A]
TAGAGTTTTCTGCGGAGCAGCGACTCGCGGTCTGACGCTCCGGAAGAAAGCTTCTGGATTTTCCTTGAAATTTTCCGGCAGGTTGAAACCAGTCATGCAC
Reverse complement sequence
GTGCATGACTGGTTTCAACCTGCCGGAAAATTTCAAGGAAAATCCAGAAGCTTTCTTCCGGAGCGTCAGACCGCGAGTCGCTGCTCCGCAGAAAACTCTA[C/T]
CGACAGAGAAACCAGCCGTACCAGCGCCACCAATTTTCAAGACTATGGCTAGCAAGACTCTCCGCGAGTTCGCTGCTCCCTCTGCTGACAATGTGGCCAT
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 | 56.40% | 5.20% | 5.52% | 32.88% | NA |
| All Indica | 2759 | 51.10% | 8.10% | 6.78% | 34.07% | NA |
| All Japonica | 1512 | 59.70% | 1.40% | 3.90% | 34.99% | NA |
| Aus | 269 | 93.30% | 0.00% | 3.72% | 2.97% | NA |
| Indica I | 595 | 45.90% | 1.80% | 5.71% | 46.55% | NA |
| Indica II | 465 | 40.90% | 3.40% | 5.59% | 50.11% | NA |
| Indica III | 913 | 59.10% | 16.20% | 7.67% | 16.98% | NA |
| Indica Intermediate | 786 | 51.70% | 6.10% | 7.25% | 34.99% | NA |
| Temperate Japonica | 767 | 75.70% | 0.00% | 0.91% | 23.34% | NA |
| Tropical Japonica | 504 | 48.40% | 2.20% | 7.94% | 41.47% | NA |
| Japonica Intermediate | 241 | 32.40% | 4.10% | 4.98% | 58.51% | NA |
| VI/Aromatic | 96 | 50.00% | 1.00% | 2.08% | 46.88% | NA |
| Intermediate | 90 | 60.00% | 1.10% | 3.33% | 35.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609173072 | G -> A | LOC_Os06g16100.1 | missense_variant ; p.Pro33Ser; MODERATE | nonsynonymous_codon ; P33S | Average:10.74; most accessible tissue: Callus, score: 29.229 | possibly damaging  |
1.739 |
TOLERATED | 0.12 |
| vg0609173072 | G -> DEL | LOC_Os06g16100.1 | N | frameshift_variant | Average:10.74; most accessible tissue: Callus, score: 29.229 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0609173072 | 4.63E-06 | 4.62E-06 | mr1474_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 |