Search for Variation information by Variation ID:
Detailed information for vg0300824792:
| Variant ID: vg0300824792 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 824792 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 291. )
Flanking Sequence (100 bp) in Reference Genome:
TCCTTCCTGCGGGCAAACGCTGACGTCTTCGCATGGAGACCGGCGGATATGCCCGGGGTCCCCAGGGAGGTGATTGAGCACCGTCTCGCCGTGCGGCCGG[G/A]
TGCAAGGCCGGTCCGGCAGAAAGTGCGGCGGCAGGCCCCGGAACGTCAAGCCTTCATCCGCGAGGAGGTGGCGCGACTTCTGGAGGCCGGATTCATCCGT
Reverse complement sequence
ACGGATGAATCCGGCCTCCAGAAGTCGCGCCACCTCCTCGCGGATGAAGGCTTGACGTTCCGGGGCCTGCCGCCGCACTTTCTGCCGGACCGGCCTTGCA[C/T]
CCGGCCGCACGGCGAGACGGTGCTCAATCACCTCCCTGGGGACCCCGGGCATATCCGCCGGTCTCCATGCGAAGACGTCAGCGTTTGCCCGCAGGAAGGA
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 | 13.40% | 0.10% | 1.12% | 85.38% | NA |
| All Indica | 2759 | 1.70% | 0.10% | 1.16% | 96.99% | NA |
| All Japonica | 1512 | 37.20% | 0.00% | 0.13% | 62.70% | NA |
| Aus | 269 | 1.90% | 0.40% | 0.00% | 97.77% | NA |
| Indica I | 595 | 0.70% | 0.00% | 1.18% | 98.15% | NA |
| Indica II | 465 | 3.90% | 0.20% | 0.43% | 95.48% | NA |
| Indica III | 913 | 2.00% | 0.30% | 1.75% | 95.95% | NA |
| Indica Intermediate | 786 | 0.90% | 0.00% | 0.89% | 98.22% | NA |
| Temperate Japonica | 767 | 60.80% | 0.00% | 0.26% | 38.98% | NA |
| Tropical Japonica | 504 | 6.50% | 0.00% | 0.00% | 93.45% | NA |
| Japonica Intermediate | 241 | 26.10% | 0.00% | 0.00% | 73.86% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 17.71% | 78.12% | NA |
| Intermediate | 90 | 16.70% | 0.00% | 2.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0300824792 | G -> A | LOC_Os03g02350.1 | missense_variant ; p.Gly824Asp; MODERATE | nonsynonymous_codon ; G824D | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.742 |
DELETERIOUS | 0.01 |
| vg0300824792 | G -> DEL | LOC_Os03g02350.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |