Search for Variation information by Variation ID:
Detailed information for vg0622630936:
| Variant ID: vg0622630936 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 22630936 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GATTCATGCCAATTGTTGTATTCCTTCGACTATGCATCAGTGCTTGATTCAGTGGCAATGTGACAAGATAGAGGTTGTGCCAGCCGACCGGTCAGTCAAT[G/A]
TTGCCAATGCCGATTTAGCTCTCTAGGAAATGGATGGCCTTGATTGTTTATCTGGAAAAGTCTGGGATGGAGATTTTCTAAAAGTGTCCGATTCTGACAT
Reverse complement sequence
ATGTCAGAATCGGACACTTTTAGAAAATCTCCATCCCAGACTTTTCCAGATAAACAATCAAGGCCATCCATTTCCTAGAGAGCTAAATCGGCATTGGCAA[C/T]
ATTGACTGACCGGTCGGCTGGCACAACCTCTATCTTGTCACATTGCCACTGAATCAAGCACTGATGCATAGTCGAAGGAATACAACAATTGGCATGAATC
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 | 76.60% | 0.80% | 4.49% | 18.18% | NA |
| All Indica | 2759 | 86.50% | 0.50% | 1.85% | 11.13% | NA |
| All Japonica | 1512 | 62.70% | 1.20% | 10.32% | 25.79% | NA |
| Aus | 269 | 45.40% | 0.40% | 1.12% | 53.16% | NA |
| Indica I | 595 | 93.80% | 0.00% | 1.34% | 4.87% | NA |
| Indica II | 465 | 89.50% | 0.00% | 0.22% | 10.32% | NA |
| Indica III | 913 | 79.40% | 1.00% | 3.40% | 16.21% | NA |
| Indica Intermediate | 786 | 87.40% | 0.80% | 1.40% | 10.43% | NA |
| Temperate Japonica | 767 | 83.30% | 0.50% | 1.69% | 14.47% | NA |
| Tropical Japonica | 504 | 33.70% | 2.40% | 20.63% | 43.25% | NA |
| Japonica Intermediate | 241 | 57.70% | 0.80% | 16.18% | 25.31% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 74.40% | 2.20% | 2.22% | 21.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0622630936 | G -> A | LOC_Os06g38240.1 | missense_variant ; p.Val1031Ile; MODERATE | nonsynonymous_codon ; V1031I | Average:17.352; most accessible tissue: Callus, score: 40.898 | benign  |
0.344 |
TOLERATED | 0.10 |
| vg0622630936 | G -> DEL | LOC_Os06g38240.1 | N | frameshift_variant | Average:17.352; most accessible tissue: Callus, score: 40.898 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0622630936 | 3.40E-06 | 3.39E-06 | mr1258 | 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 |