Search for Variation information by Variation ID:
Detailed information for vg0221510153:
| Variant ID: vg0221510153 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21510153 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTCCCTGACCTCGGCTACTTGGAAGAGCGAAGGCGGCGCGCGGCCCTTCGAGCCGCGCGCTACCAGCAGAGCCTGCGGCGCTACCATCAGCGCCACGTCC[G/A]
GGCCCGATCACTCTGCGTCGACGACCTCGTCCTACGCCGCGTCCAAACGCGTGCTGGATTGAGCAAGCTCTCACCAATGTGGGAGGGTCCGTATCGAGTG
Reverse complement sequence
CACTCGATACGGACCCTCCCACATTGGTGAGAGCTTGCTCAATCCAGCACGCGTTTGGACGCGGCGTAGGACGAGGTCGTCGACGCAGAGTGATCGGGCC[C/T]
GGACGTGGCGCTGATGGTAGCGCCGCAGGCTCTGCTGGTAGCGCGCGGCTCGAAGGGCCGCGCGCCGCCTTCGCTCTTCCAAGTAGCCGAGGTCAGGGAG
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 | 33.70% | 0.90% | 1.82% | 63.61% | NA |
| All Indica | 2759 | 2.10% | 0.10% | 2.03% | 95.76% | NA |
| All Japonica | 1512 | 95.90% | 0.30% | 0.33% | 3.44% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.00% | 99.63% | NA |
| Indica I | 595 | 1.80% | 0.00% | 0.34% | 97.82% | NA |
| Indica II | 465 | 1.70% | 0.60% | 5.16% | 92.47% | NA |
| Indica III | 913 | 1.90% | 0.10% | 1.20% | 96.82% | NA |
| Indica Intermediate | 786 | 2.70% | 0.00% | 2.42% | 94.91% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.13% | 1.30% | NA |
| Tropical Japonica | 504 | 92.50% | 0.20% | 0.40% | 6.94% | NA |
| Japonica Intermediate | 241 | 94.60% | 1.70% | 0.83% | 2.90% | NA |
| VI/Aromatic | 96 | 40.60% | 29.20% | 21.88% | 8.33% | NA |
| Intermediate | 90 | 51.10% | 4.40% | 4.44% | 40.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221510153 | G -> A | LOC_Os02g35800.1 | missense_variant ; p.Arg475Gln; MODERATE | nonsynonymous_codon ; R475Q | Average:6.451; most accessible tissue: Minghui63 root, score: 15.664 | benign  |
0.585 |
DELETERIOUS | 0.01 |
| vg0221510153 | G -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:6.451; most accessible tissue: Minghui63 root, score: 15.664 | N | N | N | N |