Search for Variation information by Variation ID:
Detailed information for vg0209796925:
| Variant ID: vg0209796925 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9796925 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 336. )
Flanking Sequence (100 bp) in Reference Genome:
TTGTACGATACAATCGCGGAGGGAAGCAGCCAGTACTGGAATGAAGAAGAGGGGAACGAGGATCCAAACCAGTACTTGAACGAGGAAGGGAACGTGGAGA[G/A]
GGATGCGGAGGGGAACCAGCAGGGGCACGTGGAAAGGGATGTGGAGGGGAACCAGGAGGAGGAGGCTAGTGGTAGTCAACCCTCCGTTGGACAGAAGAGG
Reverse complement sequence
CCTCTTCTGTCCAACGGAGGGTTGACTACCACTAGCCTCCTCCTCCTGGTTCCCCTCCACATCCCTTTCCACGTGCCCCTGCTGGTTCCCCTCCGCATCC[C/T]
TCTCCACGTTCCCTTCCTCGTTCAAGTACTGGTTTGGATCCTCGTTCCCCTCTTCTTCATTCCAGTACTGGCTGCTTCCCTCCGCGATTGTATCGTACAA
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 | 66.80% | 0.30% | 1.76% | 31.15% | NA |
| All Indica | 2759 | 51.60% | 0.00% | 2.68% | 45.67% | NA |
| All Japonica | 1512 | 97.90% | 0.90% | 0.13% | 0.99% | NA |
| Aus | 269 | 37.50% | 0.00% | 1.86% | 60.59% | NA |
| Indica I | 595 | 57.10% | 0.00% | 2.18% | 40.67% | NA |
| Indica II | 465 | 48.60% | 0.00% | 3.23% | 48.17% | NA |
| Indica III | 913 | 52.00% | 0.00% | 1.75% | 46.22% | NA |
| Indica Intermediate | 786 | 48.90% | 0.00% | 3.82% | 47.33% | NA |
| Temperate Japonica | 767 | 98.80% | 0.00% | 0.00% | 1.17% | NA |
| Tropical Japonica | 504 | 95.80% | 2.80% | 0.40% | 0.99% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 0.00% | 12.50% | NA |
| Intermediate | 90 | 71.10% | 2.20% | 2.22% | 24.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0209796925 | G -> A | LOC_Os02g17110.1 | missense_variant ; p.Arg43Lys; MODERATE | nonsynonymous_codon ; R43K | Average:5.689; most accessible tissue: Zhenshan97 flower, score: 12.818 | benign  |
1.217 |
DELETERIOUS | 0.00 |
| vg0209796925 | G -> DEL | LOC_Os02g17110.1 | N | frameshift_variant | Average:5.689; most accessible tissue: Zhenshan97 flower, score: 12.818 | N | N | N | N |