Search for Variation information by Variation ID:
Detailed information for vg0409854364:
| Variant ID: vg0409854364 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9854364 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGCCTCATTGCCAAATTCCATCTCAGTCGGCAGCAACTGAAGAAACAAGGTGCTGTGACACCTGTAATGGGCCTATGGGCTTGTAACCTCATTTGGGACC[C/T]
CGGCCCAGGTGGGGCCCATGTGGGGTGCGCCCCAAGCTGGTGGAGCACGACCCTAGGCACCCCTAGGTCGTCCTCCCACCCCTATATATAGCTAGTTACC
Reverse complement sequence
GGTAACTAGCTATATATAGGGGTGGGAGGACGACCTAGGGGTGCCTAGGGTCGTGCTCCACCAGCTTGGGGCGCACCCCACATGGGCCCCACCTGGGCCG[G/A]
GGTCCCAAATGAGGTTACAAGCCCATAGGCCCATTACAGGTGTCACAGCACCTTGTTTCTTCAGTTGCTGCCGACTGAGATGGAATTTGGCAATGAGGCT
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 | 10.40% | 0.10% | 18.18% | 71.29% | NA |
| All Indica | 2759 | 6.10% | 0.20% | 11.31% | 82.42% | NA |
| All Japonica | 1512 | 19.80% | 0.00% | 33.93% | 46.30% | NA |
| Aus | 269 | 5.90% | 0.00% | 5.20% | 88.85% | NA |
| Indica I | 595 | 5.50% | 0.00% | 8.07% | 86.39% | NA |
| Indica II | 465 | 7.70% | 0.00% | 6.67% | 85.59% | NA |
| Indica III | 913 | 6.20% | 0.40% | 15.12% | 78.20% | NA |
| Indica Intermediate | 786 | 5.30% | 0.10% | 12.09% | 82.44% | NA |
| Temperate Japonica | 767 | 24.00% | 0.00% | 58.54% | 17.47% | NA |
| Tropical Japonica | 504 | 1.60% | 0.00% | 2.58% | 95.83% | NA |
| Japonica Intermediate | 241 | 44.40% | 0.00% | 21.16% | 34.44% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 4.17% | 94.79% | NA |
| Intermediate | 90 | 10.00% | 0.00% | 17.78% | 72.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409854364 | C -> DEL | LOC_Os04g17920.1 | N | frameshift_variant | Average:5.042; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0409854364 | C -> T | LOC_Os04g17920.1 | missense_variant ; p.Pro565Leu; MODERATE | nonsynonymous_codon ; P565L | Average:5.042; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | possibly damaging  |
1.728 |
TOLERATED | 0.10 |