Search for Variation information by Variation ID:
Detailed information for vg0720240120:
| Variant ID: vg0720240120 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 20240120 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CACGTCGATGTCGTTACCAGGTTGCTTGGGGCCTTGAATAATAATCGGCATCATTATGTACTTCCTCTTCATGCATAGCCAGGGGGGAGGTTGTAGATAC[A/T]
CATCGTAACGGGCCAAGTGCTATGGCCGCTGCTCATCTCTCCAAAAGGATTCATGCCATCCGTACTCAAACCAAACCGTATGTTTCGTGCGTCCTTTCCA
Reverse complement sequence
TGGAAAGGACGCACGAAACATACGGTTTGGTTTGAGTACGGATGGCATGAATCCTTTTGGAGAGATGAGCAGCGGCCATAGCACTTGGCCCGTTACGATG[T/A]
GTATCTACAACCTCCCCCCTGGCTATGCATGAAGAGGAAGTACATAATGATGCCGATTATTATTCAAGGCCCCAAGCAACCTGGTAACGACATCGACGTG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 22.50% | 0.10% | 15.57% | 61.83% | NA |
| All Indica | 2759 | 2.10% | 0.00% | 17.33% | 80.54% | NA |
| All Japonica | 1512 | 64.90% | 0.50% | 9.72% | 24.93% | NA |
| Aus | 269 | 0.70% | 0.00% | 16.73% | 82.53% | NA |
| Indica I | 595 | 2.40% | 0.00% | 10.59% | 87.06% | NA |
| Indica II | 465 | 3.20% | 0.00% | 13.76% | 83.01% | NA |
| Indica III | 913 | 0.30% | 0.00% | 23.88% | 75.79% | NA |
| Indica Intermediate | 786 | 3.40% | 0.00% | 16.92% | 79.64% | NA |
| Temperate Japonica | 767 | 94.30% | 0.90% | 1.69% | 3.13% | NA |
| Tropical Japonica | 504 | 16.30% | 0.00% | 24.80% | 58.93% | NA |
| Japonica Intermediate | 241 | 73.00% | 0.00% | 3.73% | 23.24% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 52.08% | 45.83% | NA |
| Intermediate | 90 | 18.90% | 0.00% | 17.78% | 63.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0720240120 | A -> DEL | LOC_Os07g33820.1 | N | frameshift_variant | Average:5.785; most accessible tissue: Zhenshan97 young leaf, score: 14.714 | N | N | N | N |
| vg0720240120 | A -> T | LOC_Os07g33820.1 | missense_variant ; p.Cys361Ser; MODERATE | nonsynonymous_codon ; C361S | Average:5.785; most accessible tissue: Zhenshan97 young leaf, score: 14.714 | benign  |
1.298 |
DELETERIOUS | 0.00 |