Search for Variation information by Variation ID:
Detailed information for vg0725421273:
| Variant ID: vg0725421273 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25421273 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTGAGGCGTGCTGCCGTCGCCGTAGACGAGGAGGCGACGCTCCCCATCTCGCCGTTCTCCTGCATCACCTGCGACTGGTGATGCCACGGATTTGTCGACC[C/T]
TCTGAAGCGCCTCCCCCTGCTTAGGGCTTTGGCGCGGAGGAGGTGGAGGAGTACGAGCTCGACGGCGTGGATTCGGCTCCCCGTCGTCGCCGCTCACACT
Reverse complement sequence
AGTGTGAGCGGCGACGACGGGGAGCCGAATCCACGCCGTCGAGCTCGTACTCCTCCACCTCCTCCGCGCCAAAGCCCTAAGCAGGGGGAGGCGCTTCAGA[G/A]
GGTCGACAAATCCGTGGCATCACCAGTCGCAGGTGATGCAGGAGAACGGCGAGATGGGGAGCGTCGCCTCCTCGTCTACGGCGACGGCAGCACGCCTCAG
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 | 26.30% | 0.10% | 2.41% | 71.22% | NA |
| All Indica | 2759 | 7.60% | 0.10% | 2.61% | 89.63% | NA |
| All Japonica | 1512 | 60.60% | 0.00% | 2.25% | 37.10% | NA |
| Aus | 269 | 3.00% | 0.00% | 1.86% | 95.17% | NA |
| Indica I | 595 | 8.10% | 0.00% | 0.00% | 91.93% | NA |
| Indica II | 465 | 4.70% | 0.00% | 1.08% | 94.19% | NA |
| Indica III | 913 | 9.00% | 0.40% | 5.04% | 85.54% | NA |
| Indica Intermediate | 786 | 7.40% | 0.00% | 2.67% | 89.95% | NA |
| Temperate Japonica | 767 | 90.00% | 0.00% | 0.00% | 10.04% | NA |
| Tropical Japonica | 504 | 14.10% | 0.00% | 6.35% | 79.56% | NA |
| Japonica Intermediate | 241 | 64.70% | 0.00% | 0.83% | 34.44% | NA |
| VI/Aromatic | 96 | 76.00% | 0.00% | 0.00% | 23.96% | NA |
| Intermediate | 90 | 36.70% | 1.10% | 3.33% | 58.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725421273 | C -> DEL | LOC_Os07g42460.1 | N | frameshift_variant | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0725421273 | C -> T | LOC_Os07g42460.1 | missense_variant ; p.Arg46Lys; MODERATE | nonsynonymous_codon ; R46K | Average:6.77; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | benign  |
0.109 |
DELETERIOUS | 0.04 |