Search for Variation information by Variation ID:
Detailed information for vg0602220620:
| Variant ID: vg0602220620 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 2220620 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTGATGAACGAGGCGCAGGACACCCTCCGCCTTCAATACGGGAGCTGGGAGGCGGAGCTAGGGAAGAAGCTCGACGCCACCCAGGGGGTGCTTGACGCTG[C/T]
CGCTGCCCGAGAACAGCGGGCGGCGGAGACCGAAGCGGCGTCCCGGCGGCGCGAAGAGGCCCTTGAGGCGCGCGCCATGGCGCTGGAAGAGCGCGCCTGC
Reverse complement sequence
GCAGGCGCGCTCTTCCAGCGCCATGGCGCGCGCCTCAAGGGCCTCTTCGCGCCGCCGGGACGCCGCTTCGGTCTCCGCCGCCCGCTGTTCTCGGGCAGCG[G/A]
CAGCGTCAAGCACCCCCTGGGTGGCGTCGAGCTTCTTCCCTAGCTCCGCCTCCCAGCTCCCGTATTGAAGGCGGAGGGTGTCCTGCGCCTCGTTCATCAC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.60% | 0.30% | 6.31% | 92.74% | NA |
| All Indica | 2759 | 0.50% | 0.30% | 4.28% | 95.00% | NA |
| All Japonica | 1512 | 0.90% | 0.00% | 8.99% | 90.08% | NA |
| Aus | 269 | 0.00% | 2.60% | 12.27% | 85.13% | NA |
| Indica I | 595 | 0.00% | 0.00% | 1.51% | 98.49% | NA |
| Indica II | 465 | 1.10% | 0.00% | 6.24% | 92.69% | NA |
| Indica III | 913 | 0.30% | 0.20% | 5.37% | 94.09% | NA |
| Indica Intermediate | 786 | 0.60% | 0.60% | 3.94% | 94.78% | NA |
| Temperate Japonica | 767 | 1.20% | 0.00% | 3.52% | 95.31% | NA |
| Tropical Japonica | 504 | 1.00% | 0.00% | 17.86% | 81.15% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 7.88% | 92.12% | NA |
| VI/Aromatic | 96 | 1.00% | 2.10% | 4.17% | 92.71% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 7.78% | 91.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0602220620 | C -> T | LOC_Os06g05030.1 | missense_variant ; p.Ala718Val; MODERATE | nonsynonymous_codon ; A718V | Average:18.749; most accessible tissue: Minghui63 root, score: 50.524 | benign  |
1.164 |
DELETERIOUS | 0.00 |
| vg0602220620 | C -> DEL | LOC_Os06g05030.1 | N | frameshift_variant | Average:18.749; most accessible tissue: Minghui63 root, score: 50.524 | N | N | N | N |