Search for Variation information by Variation ID:
Detailed information for vg0300825981:
| Variant ID: vg0300825981 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 825981 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTTGTCAGACGGTGCTAGGAGCCCCCGACCCCCAGGAAGGCCCTGAGGCCACTGTGGGAAGGCCGCACCTATCGCCCTTTGACCCCGAGGCTAACCCTGT[G/A]
CTGACTCGACCCGGGAAAGAGCAGGGAGAAGAGGCCCCCGAGCCGAACGGAGGCCTAAGGCCCCTGACGACCGGAGTTGGCCCTTTGCCCGCTTGTCCGA
Reverse complement sequence
TCGGACAAGCGGGCAAAGGGCCAACTCCGGTCGTCAGGGGCCTTAGGCCTCCGTTCGGCTCGGGGGCCTCTTCTCCCTGCTCTTTCCCGGGTCGAGTCAG[C/T]
ACAGGGTTAGCCTCGGGGTCAAAGGGCGATAGGTGCGGCCTTCCCACAGTGGCCTCAGGGCCTTCCTGGGGGTCGGGGGCTCCTAGCACCGTCTGACAAG
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 | 17.70% | 0.20% | 2.96% | 79.14% | NA |
| All Indica | 2759 | 8.20% | 0.00% | 3.15% | 88.62% | NA |
| All Japonica | 1512 | 37.90% | 0.10% | 0.60% | 61.44% | NA |
| Aus | 269 | 4.10% | 0.00% | 0.37% | 95.54% | NA |
| Indica I | 595 | 8.60% | 0.00% | 1.68% | 89.75% | NA |
| Indica II | 465 | 11.20% | 0.00% | 4.30% | 84.52% | NA |
| Indica III | 913 | 6.80% | 0.00% | 2.08% | 91.13% | NA |
| Indica Intermediate | 786 | 7.90% | 0.00% | 4.83% | 87.28% | NA |
| Temperate Japonica | 767 | 61.50% | 0.00% | 0.26% | 38.20% | NA |
| Tropical Japonica | 504 | 7.30% | 0.00% | 0.40% | 92.26% | NA |
| Japonica Intermediate | 241 | 26.60% | 0.40% | 2.07% | 70.95% | NA |
| VI/Aromatic | 96 | 8.30% | 7.30% | 37.50% | 46.88% | NA |
| Intermediate | 90 | 20.00% | 1.10% | 7.78% | 71.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0300825981 | G -> A | LOC_Os03g02350.1 | synonymous_variant ; p.Val1220Val; LOW | nonsynonymous_codon ; V1220A | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.134 |
DELETERIOUS | 0.00 |
| vg0300825981 | G -> DEL | LOC_Os03g02350.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |