Search for Variation information by Variation ID:
Detailed information for vg0414145678:
| Variant ID: vg0414145678 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 14145678 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCCCCTCAGGGGTAGAAGCGACGAAGGTGCTCGATGTTCCATGGGTTAGGCAACTCTGTGCCGTCGCCCGTGGCCAGCCGTATGGAGCCCGGCCGGGGGA[C/T]
GCCGATCACTCGATACGGACCCTCCCACATTGGTGAGAGCTTGCTCAATCCAGCACGCGTTTGAACGCGGCGTAAGACGAGGTCGTCGACGCAGAGTGAT
Reverse complement sequence
ATCACTCTGCGTCGACGACCTCGTCTTACGCCGCGTTCAAACGCGTGCTGGATTGAGCAAGCTCTCACCAATGTGGGAGGGTCCGTATCGAGTGATCGGC[G/A]
TCCCCCGGCCGGGCTCCATACGGCTGGCCACGGGCGACGGCACAGAGTTGCCTAACCCATGGAACATCGAGCACCTTCGTCGCTTCTACCCCTGAGGGGG
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 | 24.80% | 9.90% | 1.16% | 64.18% | NA |
| All Indica | 2759 | 12.10% | 0.40% | 0.83% | 86.66% | NA |
| All Japonica | 1512 | 52.10% | 29.60% | 1.72% | 16.67% | NA |
| Aus | 269 | 6.30% | 0.00% | 0.37% | 93.31% | NA |
| Indica I | 595 | 35.30% | 0.00% | 1.18% | 63.53% | NA |
| Indica II | 465 | 3.40% | 0.90% | 0.00% | 95.70% | NA |
| Indica III | 913 | 3.10% | 0.30% | 0.88% | 95.73% | NA |
| Indica Intermediate | 786 | 10.20% | 0.50% | 1.02% | 88.30% | NA |
| Temperate Japonica | 767 | 85.30% | 2.20% | 1.96% | 10.56% | NA |
| Tropical Japonica | 504 | 7.10% | 75.80% | 1.19% | 15.87% | NA |
| Japonica Intermediate | 241 | 40.20% | 19.90% | 2.07% | 37.76% | NA |
| VI/Aromatic | 96 | 10.40% | 0.00% | 3.12% | 86.46% | NA |
| Intermediate | 90 | 24.40% | 11.10% | 2.22% | 62.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0414145678 | C -> DEL | LOC_Os04g24640.1 | N | frameshift_variant | Average:24.211; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 | N | N | N | N |
| vg0414145678 | C -> T | LOC_Os04g24640.1 | missense_variant ; p.Val476Ile; MODERATE | nonsynonymous_codon ; V476I | Average:24.211; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 | benign  |
0.416 |
DELETERIOUS | 0.01 |