Search for Variation information by Variation ID:
Detailed information for vg0512045482:
| Variant ID: vg0512045482 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12045482 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGCGGCTAATTCCTTCTCCAAACGATCCACCTTGTCTTCTAGCTTGCAAATCTTACCACGATTCCGGTCTTCACGATCTTGAGCGGCTAACACAGTCTCC[G/A]
CACGACTTTCATCCATAGCCCACAACATCTCAACCAAATGCTTCGTGGTAGCATCATTCTCAATTCCTTCAGTCTCAAGGTAACTGCCACGGTCACTTCC
Reverse complement sequence
GGAAGTGACCGTGGCAGTTACCTTGAGACTGAAGGAATTGAGAATGATGCTACCACGAAGCATTTGGTTGAGATGTTGTGGGCTATGGATGAAAGTCGTG[C/T]
GGAGACTGTGTTAGCCGCTCAAGATCGTGAAGACCGGAATCGTGGTAAGATTTGCAAGCTAGAAGACAAGGTGGATCGTTTGGAGAAGGAATTAGCCGCA
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 | 85.10% | 0.10% | 3.53% | 11.26% | NA |
| All Indica | 2759 | 87.40% | 0.00% | 5.65% | 6.96% | NA |
| All Japonica | 1512 | 91.30% | 0.40% | 0.33% | 7.94% | NA |
| Aus | 269 | 21.60% | 0.00% | 0.74% | 77.70% | NA |
| Indica I | 595 | 92.30% | 0.00% | 3.70% | 4.03% | NA |
| Indica II | 465 | 97.60% | 0.00% | 0.86% | 1.51% | NA |
| Indica III | 913 | 79.70% | 0.00% | 9.75% | 10.51% | NA |
| Indica Intermediate | 786 | 86.50% | 0.00% | 5.22% | 8.27% | NA |
| Temperate Japonica | 767 | 84.50% | 0.70% | 0.52% | 14.34% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.40% | 0.41% | 2.49% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 87.80% | 0.00% | 2.22% | 10.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512045482 | G -> DEL | LOC_Os05g20520.1 | N | frameshift_variant | Average:11.469; most accessible tissue: Zhenshan97 flower, score: 24.143 | N | N | N | N |
| vg0512045482 | G -> A | LOC_Os05g20520.1 | missense_variant ; p.Ala167Val; MODERATE | nonsynonymous_codon ; A167V | Average:11.469; most accessible tissue: Zhenshan97 flower, score: 24.143 | benign  |
0.399 |
TOLERATED | 0.24 |