Search for Variation information by Variation ID:
Detailed information for vg0719561182:
| Variant ID: vg0719561182 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19561182 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 281. )
Flanking Sequence (100 bp) in Reference Genome:
AGAGTTTATTGACGGCGTGCACTATTTTTTGAGAGTGGCCGAAGCTAACAGGCAAAGGGGTTTTATTTGTTGTCCATGCAATAAGTGTAAGAATCAGAAG[G/A]
AGTATTCTGCATCCAGGACTATTCATTTCCACTTGTTTGAGTCGGGGTTCATGCCAAGCTATAATTGTTGGACATCCCACGGAGAGCAAGGTGTTGAAAT
Reverse complement sequence
ATTTCAACACCTTGCTCTCCGTGGGATGTCCAACAATTATAGCTTGGCATGAACCCCGACTCAAACAAGTGGAAATGAATAGTCCTGGATGCAGAATACT[C/T]
CTTCTGATTCTTACACTTATTGCATGGACAACAAATAAAACCCCTTTGCCTGTTAGCTTCGGCCACTCTCAAAAAATAGTGCACGCCGTCAATAAACTCT
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 | 19.70% | 0.30% | 19.87% | 60.18% | NA |
| All Indica | 2759 | 0.90% | 0.30% | 18.01% | 80.72% | NA |
| All Japonica | 1512 | 59.00% | 0.00% | 15.21% | 25.79% | NA |
| Aus | 269 | 0.00% | 1.10% | 74.72% | 24.16% | NA |
| Indica I | 595 | 0.30% | 0.00% | 2.69% | 96.97% | NA |
| Indica II | 465 | 2.20% | 0.00% | 12.90% | 84.95% | NA |
| Indica III | 913 | 0.20% | 0.80% | 31.22% | 67.80% | NA |
| Indica Intermediate | 786 | 1.50% | 0.30% | 17.30% | 80.92% | NA |
| Temperate Japonica | 767 | 93.00% | 0.00% | 2.61% | 4.43% | NA |
| Tropical Japonica | 504 | 10.90% | 0.00% | 38.49% | 50.60% | NA |
| Japonica Intermediate | 241 | 51.50% | 0.00% | 6.64% | 41.91% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 1.04% | 98.96% | NA |
| Intermediate | 90 | 13.30% | 1.10% | 11.11% | 74.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719561182 | G -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:4.449; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0719561182 | G -> A | LOC_Os07g32740.1 | missense_variant ; p.Glu47Lys; MODERATE | nonsynonymous_codon ; E47K | Average:4.449; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.673 |
DELETERIOUS | 0.01 |