Search for Variation information by Variation ID:
Detailed information for vg0811599465:
| Variant ID: vg0811599465 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599465 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCAAGCGGAGGGCCTCGACCTCCCCGGCGGACGAGTCCAGTGCGCCCTGCGGCTCGGCGATGGTGTGTTCGGCGGCTGCGAGGCGGGCGGCTAGGTCGCC[C/A]
TGGCCCGCGGCCGCCCCGCCGCTGTGCGCTCTCGCGTCCAGCTCCTTCGCCCGCGCCTCGAGCTCAGCGGCCCGCTGATCCAGTGCGGCCCTCTCGGCGC
Reverse complement sequence
GCGCCGAGAGGGCCGCACTGGATCAGCGGGCCGCTGAGCTCGAGGCGCGGGCGAAGGAGCTGGACGCGAGAGCGCACAGCGGCGGGGCGGCCGCGGGCCA[G/T]
GGCGACCTAGCCGCCCGCCTCGCAGCCGCCGAACACACCATCGCCGAGCCGCAGGGCGCACTGGACTCGTCCGCCGGGGAGGTCGAGGCCCTCCGCTTGG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.20% | 0.20% | 4.63% | 94.96% | NA |
| All Indica | 2759 | 0.00% | 0.30% | 4.35% | 95.32% | NA |
| All Japonica | 1512 | 0.70% | 0.00% | 5.75% | 93.58% | NA |
| Aus | 269 | 0.00% | 0.00% | 3.72% | 96.28% | NA |
| Indica I | 595 | 0.00% | 0.00% | 0.50% | 99.50% | NA |
| Indica II | 465 | 0.00% | 0.00% | 0.65% | 99.35% | NA |
| Indica III | 913 | 0.00% | 0.40% | 10.30% | 89.27% | NA |
| Indica Intermediate | 786 | 0.00% | 0.60% | 2.54% | 96.82% | NA |
| Temperate Japonica | 767 | 1.00% | 0.00% | 6.78% | 92.18% | NA |
| Tropical Japonica | 504 | 0.00% | 0.00% | 4.76% | 95.24% | NA |
| Japonica Intermediate | 241 | 0.80% | 0.00% | 4.56% | 94.61% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 2.22% | 97.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599465 | C -> A | LOC_Os08g19400.1 | missense_variant ; p.Gln146His; MODERATE | nonsynonymous_codon ; Q146D | Average:19.537; most accessible tissue: Zhenshan97 flag leaf, score: 32.264 | benign  |
-0.524 |
TOLERATED | 0.59 |
| vg0811599465 | C -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:19.537; most accessible tissue: Zhenshan97 flag leaf, score: 32.264 | N | N | N | N |