Search for Variation information by Variation ID:
Detailed information for vg0135356924:
| Variant ID: vg0135356924 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 35356924 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGGGACCAACTGGTGCTCCCGCCAGCGGTAGCCCGAGCAGGTACGACACGTCCTGCAGTGTCGGAGCCATCTCCCCACAGGGAAGGTGGAACGTGTGCGT[C/A]
TCAGGTCTCCAGCGGTCTACTAGAGCGGCAAGGAGTGACCGGTCTGCATCCCACCGCTTCGCTGGGTCACGGTCGTCCGCCGCCGCCTCAACAAGCCTAC
Reverse complement sequence
GTAGGCTTGTTGAGGCGGCGGCGGACGACCGTGACCCAGCGAAGCGGTGGGATGCAGACCGGTCACTCCTTGCCGCTCTAGTAGACCGCTGGAGACCTGA[G/T]
ACGCACACGTTCCACCTTCCCTGTGGGGAGATGGCTCCGACACTGCAGGACGTGTCGTACCTGCTCGGGCTACCGCTGGCGGGAGCACCAGTTGGTCCCG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 12.30% | 0.10% | 12.53% | 75.12% | NA |
| All Indica | 2759 | 5.70% | 0.00% | 0.72% | 93.55% | NA |
| All Japonica | 1512 | 23.30% | 0.30% | 33.13% | 43.19% | NA |
| Aus | 269 | 9.70% | 0.00% | 0.00% | 90.33% | NA |
| Indica I | 595 | 10.60% | 0.00% | 0.34% | 89.08% | NA |
| Indica II | 465 | 6.90% | 0.00% | 0.22% | 92.90% | NA |
| Indica III | 913 | 0.70% | 0.00% | 0.44% | 98.90% | NA |
| Indica Intermediate | 786 | 7.30% | 0.00% | 1.65% | 91.09% | NA |
| Temperate Japonica | 767 | 14.50% | 0.40% | 31.03% | 54.11% | NA |
| Tropical Japonica | 504 | 36.90% | 0.40% | 28.37% | 34.33% | NA |
| Japonica Intermediate | 241 | 23.20% | 0.00% | 49.79% | 26.97% | NA |
| VI/Aromatic | 96 | 25.00% | 0.00% | 53.12% | 21.88% | NA |
| Intermediate | 90 | 20.00% | 0.00% | 22.22% | 57.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0135356924 | C -> A | LOC_Os01g61090.1 | missense_variant ; p.Glu970Asp; MODERATE | nonsynonymous_codon ; E970D | Average:32.934; most accessible tissue: Zhenshan97 flag leaf, score: 71.238 | benign  |
0.563 |
DELETERIOUS | 0.00 |
| vg0135356924 | C -> DEL | LOC_Os01g61090.1 | N | frameshift_variant | Average:32.934; most accessible tissue: Zhenshan97 flag leaf, score: 71.238 | N | N | N | N |