Search for Variation information by Variation ID:
Detailed information for vg0222980378:
| Variant ID: vg0222980378 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 22980378 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 263. )
Flanking Sequence (100 bp) in Reference Genome:
CCAGATGCCATAGGCGGGCTCGAACACCTGGAAGAGCTTCGCCTCGCTTCCAACGCGTTGGTCTCCCTCCCGGACTCCATAGGCCTCCTCACCAGCCTCA[A/G]
GATCCTCGACGTCTCGGGCAACAAGCTGAGGTCTCTCCCCGACAGCATCTCAAAATGCAGGTAGAATCAACCAGCCAAGGCCAAAGCACGCATCATCATC
Reverse complement sequence
GATGATGATGCGTGCTTTGGCCTTGGCTGGTTGATTCTACCTGCATTTTGAGATGCTGTCGGGGAGAGACCTCAGCTTGTTGCCCGAGACGTCGAGGATC[T/C]
TGAGGCTGGTGAGGAGGCCTATGGAGTCCGGGAGGGAGACCAACGCGTTGGAAGCGAGGCGAAGCTCTTCCAGGTGTTCGAGCCCGCCTATGGCATCTGG
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 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 54.30% | 45.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.70% | 2.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0222980378 | A -> G | LOC_Os02g38040.1 | missense_variant ; p.Lys263Arg; MODERATE | nonsynonymous_codon ; K263R | Average:71.913; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 | benign  |
0.725 |
TOLERATED | 0.22 |