Search for Variation information by Variation ID:
Detailed information for vg0300825500:
| Variant ID: vg0300825500 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 825500 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTCGGGTTCTTGGTCTCTGCCCGAGGCATTGAGGCCAACCCCGAGAAGATACGGGCTATAGAGCGGATGCGCCCCCCCAGCAAACTTAGGGATGTGCAAT[G/A]
CGTCACCGGTTGCATGGCCGCCCTAAGTCGGTTCATATCGAGGCTGGGAGAGAAGGCGTTACCCTTATTTAAGCTTCTCAAACGCTCCGGACCGTTTACC
Reverse complement sequence
GGTAAACGGTCCGGAGCGTTTGAGAAGCTTAAATAAGGGTAACGCCTTCTCTCCCAGCCTCGATATGAACCGACTTAGGGCGGCCATGCAACCGGTGACG[C/T]
ATTGCACATCCCTAAGTTTGCTGGGGGGGCGCATCCGCTCTATAGCCCGTATCTTCTCGGGGTTGGCCTCAATGCCTCGGGCAGAGACCAAGAACCCGAG
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 | 12.10% | 0.60% | 0.85% | 86.48% | NA |
| All Indica | 2759 | 1.10% | 0.00% | 0.33% | 98.55% | NA |
| All Japonica | 1512 | 34.30% | 1.70% | 1.26% | 62.70% | NA |
| Aus | 269 | 1.50% | 0.00% | 0.00% | 98.51% | NA |
| Indica I | 595 | 0.70% | 0.00% | 0.34% | 98.99% | NA |
| Indica II | 465 | 3.90% | 0.00% | 0.43% | 95.70% | NA |
| Indica III | 913 | 0.50% | 0.00% | 0.22% | 99.23% | NA |
| Indica Intermediate | 786 | 0.50% | 0.00% | 0.38% | 99.11% | NA |
| Temperate Japonica | 767 | 58.70% | 0.40% | 1.96% | 38.98% | NA |
| Tropical Japonica | 504 | 1.40% | 4.40% | 0.60% | 93.65% | NA |
| Japonica Intermediate | 241 | 25.70% | 0.40% | 0.41% | 73.44% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 12.50% | 85.42% | NA |
| Intermediate | 90 | 18.90% | 0.00% | 0.00% | 81.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0300825500 | G -> A | LOC_Os03g02350.1 | missense_variant ; p.Cys1060Tyr; MODERATE | nonsynonymous_codon ; C1060Y | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.848 |
DELETERIOUS | 0.01 |
| vg0300825500 | G -> DEL | LOC_Os03g02350.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |