Search for Variation information by Variation ID:
Detailed information for vg0607895107:
| Variant ID: vg0607895107 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7895107 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGCGCACGAGGCTGCCTGCGCCGAAGAAGAGCTCGCGCTCCGCCTCCGCGAGGACGCGCTCACCGAGCGGGAGCGAGCTCTCGAGGGGGCCGAGGCCGCG[G/A]
CGCAACAGCTGGCGGACAGCCTGTCCCTCCGCGAGGCAGCGCAGGAGGAGCAGGCGCGCCGCAATCTGGAAGGTGCCCGCGCCGAGAGGGCCGCACTGAA
Reverse complement sequence
TTCAGTGCGGCCCTCTCGGCGCGGGCACCTTCCAGATTGCGGCGCGCCTGCTCCTCCTGCGCTGCCTCGCGGAGGGACAGGCTGTCCGCCAGCTGTTGCG[C/T]
CGCGGCCTCGGCCCCCTCGAGAGCTCGCTCCCGCTCGGTGAGCGCGTCCTCGCGGAGGCGGAGCGCGAGCTCTTCTTCGGCGCAGGCAGCCTCGTGCGCC
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 | 0.40% | 0.20% | 5.37% | 94.10% | NA |
| All Indica | 2759 | 0.60% | 0.00% | 0.29% | 99.13% | NA |
| All Japonica | 1512 | 0.00% | 0.50% | 15.28% | 84.19% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.74% | 98.88% | NA |
| Indica I | 595 | 0.50% | 0.00% | 0.00% | 99.50% | NA |
| Indica II | 465 | 0.20% | 0.00% | 0.22% | 99.57% | NA |
| Indica III | 913 | 1.10% | 0.00% | 0.33% | 98.58% | NA |
| Indica Intermediate | 786 | 0.30% | 0.00% | 0.51% | 99.24% | NA |
| Temperate Japonica | 767 | 0.00% | 0.90% | 26.60% | 72.49% | NA |
| Tropical Japonica | 504 | 0.00% | 0.20% | 1.79% | 98.02% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 7.47% | 92.53% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 7.29% | 92.71% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 6.67% | 93.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607895107 | G -> A | LOC_Os06g14150.1 | missense_variant ; p.Ala859Thr; MODERATE | nonsynonymous_codon ; A859T | Average:5.819; most accessible tissue: Zhenshan97 panicle, score: 16.188 | possibly damaging  |
1.571 |
TOLERATED | 0.25 |
| vg0607895107 | G -> DEL | LOC_Os06g14150.1 | N | frameshift_variant | Average:5.819; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |