Search for Variation information by Variation ID:
Detailed information for vg0135356943:
| Variant ID: vg0135356943 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 35356943 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGCCAGCGGTAGCCCGAGCAGGTACGACACGTCCTGCAGTGTCGGAGCCATCTCCCCACAGGGAAGGTGGAACGTGTGCGTCTCAGGTCTCCAGCGGTCT[A/G]
CTAGAGCGGCAAGGAGTGACCGGTCTGCATCCCACCGCTTCGCTGGGTCACGGTCGTCCGCCGCCGCCTCAACAAGCCTACAAAGTGGTAGAAGGCCTGC
Reverse complement sequence
GCAGGCCTTCTACCACTTTGTAGGCTTGTTGAGGCGGCGGCGGACGACCGTGACCCAGCGAAGCGGTGGGATGCAGACCGGTCACTCCTTGCCGCTCTAG[T/C]
AGACCGCTGGAGACCTGAGACGCACACGTTCCACCTTCCCTGTGGGGAGATGGCTCCGACACTGCAGGACGTGTCGTACCTGCTCGGGCTACCGCTGGCG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 7.60% | 0.60% | 15.87% | 75.96% | NA |
| All Indica | 2759 | 1.10% | 0.80% | 0.58% | 97.61% | NA |
| All Japonica | 1512 | 19.40% | 0.00% | 43.52% | 37.10% | NA |
| Aus | 269 | 0.00% | 3.00% | 0.00% | 97.03% | NA |
| Indica I | 595 | 2.20% | 0.80% | 1.01% | 95.97% | NA |
| Indica II | 465 | 0.40% | 1.30% | 0.22% | 98.06% | NA |
| Indica III | 913 | 0.10% | 0.20% | 0.11% | 99.56% | NA |
| Indica Intermediate | 786 | 1.70% | 1.00% | 1.02% | 96.31% | NA |
| Temperate Japonica | 767 | 12.30% | 0.00% | 40.81% | 46.94% | NA |
| Tropical Japonica | 504 | 28.80% | 0.00% | 46.03% | 25.20% | NA |
| Japonica Intermediate | 241 | 22.40% | 0.00% | 46.89% | 30.71% | NA |
| VI/Aromatic | 96 | 26.00% | 0.00% | 47.92% | 26.04% | NA |
| Intermediate | 90 | 11.10% | 0.00% | 33.33% | 55.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0135356943 | A -> G | LOC_Os01g61090.1 | missense_variant ; p.Val964Ala; MODERATE | nonsynonymous_codon ; V964A | Average:32.766; most accessible tissue: Zhenshan97 flag leaf, score: 70.837 | benign  |
0.857 |
DELETERIOUS | 0.03 |
| vg0135356943 | A -> DEL | LOC_Os01g61090.1 | N | frameshift_variant | Average:32.766; most accessible tissue: Zhenshan97 flag leaf, score: 70.837 | N | N | N | N |