Search for Variation information by Variation ID:
Detailed information for vg0620602930:
| Variant ID: vg0620602930 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20602930 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 272. )
Flanking Sequence (100 bp) in Reference Genome:
CGGTGCAGCCTGTCCAGATTCACTAATTTAGTGCAGTCCGGACCAACCCTATCCTTACCCGAATATGTGCTACTGCAACATTTCCATATAGGTTTGGATA[A/G]
GGAGTCTGCATTCTATCTGGACATAACCGTCGGAGGATCGTTGATGCACAAAACGCCGTCGGAAGGAAGAACAATTTTGGATCATATTCTAGAAAATACT
Reverse complement sequence
AGTATTTTCTAGAATATGATCCAAAATTGTTCTTCCTTCCGACGGCGTTTTGTGCATCAACGATCCTCCGACGGTTATGTCCAGATAGAATGCAGACTCC[T/C]
TATCCAAACCTATATGGAAATGTTGCAGTAGCACATATTCGGGTAAGGATAGGGTTGGTCCGGACTGCACTAAATTAGTGAATCTGGACAGGCTGCACCG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.60% | 0.10% | 0.08% | 1.18% | NA |
| All Indica | 2759 | 99.60% | 0.30% | 0.11% | 0.07% | NA |
| All Japonica | 1512 | 96.50% | 0.00% | 0.07% | 3.44% | 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 | 98.80% | 0.80% | 0.33% | 0.11% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.20% | 0.99% | NA |
| Japonica Intermediate | 241 | 83.00% | 0.00% | 0.00% | 17.01% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 0.00% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620602930 | A -> G | LOC_Os06g35340.1 | missense_variant ; p.Lys125Arg; MODERATE | nonsynonymous_codon ; K125R | Average:13.336; most accessible tissue: Minghui63 flag leaf, score: 17.373 | benign  |
0.392 |
TOLERATED | 0.39 |
| vg0620602930 | A -> DEL | LOC_Os06g35340.1 | N | frameshift_variant | Average:13.336; most accessible tissue: Minghui63 flag leaf, score: 17.373 | N | N | N | N |