Search for Variation information by Variation ID:
Detailed information for vg0607893822:
| Variant ID: vg0607893822 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7893822 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTGTATTCATTCTCTCAACGCGAGTTTTCACTCACCCATCTTGTTCGTCTTCTGGTCTTTTCTTTTGTTTCAGCGAGATCCCGTCGCGTCCCTCCCGCCA[T/G]
TCCAAGTCCGGCCAGTCTGAGGCCGAGGATCCGGCGACCGCAGAGGCCCGCAGGCGGCAAGCTGACCGGCGAGAGGCCGCGGATCGCCTACGGGAAGCCG
Reverse complement sequence
CGGCTTCCCGTAGGCGATCCGCGGCCTCTCGCCGGTCAGCTTGCCGCCTGCGGGCCTCTGCGGTCGCCGGATCCTCGGCCTCAGACTGGCCGGACTTGGA[A/C]
TGGCGGGAGGGACGCGACGGGATCTCGCTGAAACAAAAGAAAAGACCAGAAGACGAACAAGATGGGTGAGTGAAAACTCGCGTTGAGAGAATGAATACAG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 7.00% | 0.40% | 1.65% | 90.96% | NA |
| All Indica | 2759 | 0.60% | 0.60% | 1.23% | 97.57% | NA |
| All Japonica | 1512 | 20.00% | 0.00% | 0.53% | 79.50% | NA |
| Aus | 269 | 0.70% | 0.40% | 12.64% | 86.25% | NA |
| Indica I | 595 | 0.30% | 0.30% | 0.84% | 98.49% | NA |
| Indica II | 465 | 0.60% | 0.00% | 0.22% | 99.14% | NA |
| Indica III | 913 | 0.90% | 1.20% | 2.30% | 95.62% | NA |
| Indica Intermediate | 786 | 0.50% | 0.40% | 0.89% | 98.22% | NA |
| Temperate Japonica | 767 | 34.30% | 0.00% | 0.26% | 65.45% | NA |
| Tropical Japonica | 504 | 2.80% | 0.00% | 1.19% | 96.03% | NA |
| Japonica Intermediate | 241 | 10.40% | 0.00% | 0.00% | 89.63% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 2.08% | 96.88% | NA |
| Intermediate | 90 | 11.10% | 0.00% | 0.00% | 88.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607893822 | T -> G | LOC_Os06g14150.1 | missense_variant ; p.His430Gln; MODERATE | nonsynonymous_codon ; H430Q | Average:7.421; most accessible tissue: Callus, score: 21.877 | possibly damaging  |
1.781 |
TOLERATED | 0.06 |
| vg0607893822 | T -> DEL | LOC_Os06g14150.1 | N | frameshift_variant | Average:7.421; most accessible tissue: Callus, score: 21.877 | N | N | N | N |