Search for Variation information by Variation ID:
Detailed information for vg0623793079:
| Variant ID: vg0623793079 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 23793079 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AAGTTCTTGCGGCTTATTTCATCATCCTTGGCCCGAAGACGGTTCTTAAAACCATCAAAACGGGCCCGCACGGTTCGCTCCGTCGAACAGTGAGCCGCAA[A/G]
AATCTAAATGAAAGATAGGAGCGGGCGAAAAGAACGAAAGGTTAATTGCGAGACGTAAAAATAAGAGGGAAGAGGAAAACGAAGAGGGAAGAAAGGGCAT
Reverse complement sequence
ATGCCCTTTCTTCCCTCTTCGTTTTCCTCTTCCCTCTTATTTTTACGTCTCGCAATTAACCTTTCGTTCTTTTCGCCCGCTCCTATCTTTCATTTAGATT[T/C]
TTGCGGCTCACTGTTCGACGGAGCGAACCGTGCGGGCCCGTTTTGATGGTTTTAAGAACCGTCTTCGGGCCAAGGATGATGAAATAAGCCGCAAGAACTT
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 | 79.70% | 19.20% | 0.83% | 0.25% | NA |
| All Indica | 2759 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 44.40% | 52.20% | 2.58% | 0.79% | NA |
| Aus | 269 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 21.90% | 71.80% | 4.69% | 1.56% | NA |
| Tropical Japonica | 504 | 86.50% | 13.30% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 27.80% | 71.40% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 18.80% | 81.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 77.80% | 22.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0623793079 | A -> G | LOC_Os06g40000.1 | missense_variant ; p.Phe556Leu; MODERATE | nonsynonymous_codon ; F556L | Average:56.805; most accessible tissue: Minghui63 flag leaf, score: 85.67 | probably damaging  |
-2.149 |
TOLERATED | 1.00 |
| vg0623793079 | A -> DEL | LOC_Os06g40000.1 | N | frameshift_variant | Average:56.805; most accessible tissue: Minghui63 flag leaf, score: 85.67 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0623793079 | 4.89E-06 | NA | mr1889 | 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 |