Search for Variation information by Variation ID:
Detailed information for vg0811599240:
| Variant ID: vg0811599240 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599240 |
| Reference Allele: C | Alternative Allele: T,A |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCTCCACCGCCCCCCGGGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAGCTCCTCGGGGAGCCGCTTGAGGGTCCCGGCCATCTCTGAGAGGCG[C/T,A]
TGGGCGAGGCCCCCCTGGTTGGCGGCGTACTTCGCGTACCGCCCGCCCCAGAGGCCCGCCTGCCGCCCGGCACGGTCTAGACGGGAGACGGCATCCCGAA
Reverse complement sequence
TTCGGGATGCCGTCTCCCGTCTAGACCGTGCCGGGCGGCAGGCGGGCCTCTGGGGCGGGCGGTACGCGAAGTACGCCGCCAACCAGGGGGGCCTCGCCCA[G/A,T]
CGCCTCTCAGAGATGGCCGGGACCCTCAAGCGGCTCCCCGAGGAGCTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCCCGGGGGGCGGTGGAGC
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 | 47.00% | 0.50% | 3.24% | 49.07% | A: 0.23% |
| All Indica | 2759 | 52.40% | 0.40% | 2.72% | 44.15% | A: 0.40% |
| All Japonica | 1512 | 36.40% | 0.70% | 4.63% | 58.27% | NA |
| Aus | 269 | 51.70% | 1.10% | 1.12% | 46.10% | NA |
| Indica I | 595 | 31.30% | 0.70% | 4.54% | 63.53% | NA |
| Indica II | 465 | 35.10% | 0.00% | 3.66% | 60.65% | A: 0.65% |
| Indica III | 913 | 76.70% | 0.40% | 1.53% | 20.70% | A: 0.66% |
| Indica Intermediate | 786 | 50.40% | 0.30% | 2.16% | 46.95% | A: 0.25% |
| Temperate Japonica | 767 | 27.80% | 0.10% | 5.74% | 66.36% | NA |
| Tropical Japonica | 504 | 47.80% | 1.00% | 3.97% | 47.22% | NA |
| Japonica Intermediate | 241 | 40.20% | 1.70% | 2.49% | 55.60% | NA |
| VI/Aromatic | 96 | 49.00% | 0.00% | 2.08% | 48.96% | NA |
| Intermediate | 90 | 42.20% | 0.00% | 3.33% | 54.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599240 | C -> T | LOC_Os08g19400.1 | synonymous_variant ; p.Gln221Gln; LOW | synonymous_codon | Average:20.387; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | N | N | N | N |
| vg0811599240 | C -> A | LOC_Os08g19400.1 | missense_variant ; p.Gln221His; MODERATE | nonsynonymous_codon ; Q221H | Average:20.387; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | probably damaging  |
2.477 |
DELETERIOUS | 0.00 |
| vg0811599240 | C -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:20.387; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | N | N | N | N |