Search for Variation information by Variation ID:
Detailed information for vg0318608583:
| Variant ID: vg0318608583 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18608583 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCATATAGAAAAAAAATTCAAAGGTGGTGCCGGTGATTGCAAAGCGAGCGCTCGGGGCGGGGCGGGGAGGGGCGTACCTTGGAGTCCGCGACGAGGCGGA[C/A]
GTAGTCCCAGCTGAGGACGATCTTGTGGAAGCGGTCCATGGTGGAGGCGGCGACGCCCGACGAGGAGGAGGAGGCGCCGCCTCCGCCTCCGCCGCCGCCG
Reverse complement sequence
CGGCGGCGGCGGAGGCGGAGGCGGCGCCTCCTCCTCCTCGTCGGGCGTCGCCGCCTCCACCATGGACCGCTTCCACAAGATCGTCCTCAGCTGGGACTAC[G/T]
TCCGCCTCGTCGCGGACTCCAAGGTACGCCCCTCCCCGCCCCGCCCCGAGCGCTCGCTTTGCAATCACCGGCACCACCTTTGAATTTTTTTTCTATATGG
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 | 88.20% | 0.60% | 8.70% | 2.54% | NA |
| All Indica | 2759 | 86.50% | 0.50% | 12.40% | 0.62% | NA |
| All Japonica | 1512 | 89.00% | 0.90% | 3.51% | 6.68% | NA |
| Aus | 269 | 95.50% | 0.40% | 4.09% | 0.00% | NA |
| Indica I | 595 | 66.40% | 1.00% | 32.44% | 0.17% | NA |
| Indica II | 465 | 95.90% | 0.20% | 1.51% | 2.37% | NA |
| Indica III | 913 | 93.60% | 0.50% | 5.59% | 0.22% | NA |
| Indica Intermediate | 786 | 87.80% | 0.30% | 11.58% | 0.38% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 73.00% | 1.20% | 8.13% | 17.66% | NA |
| Japonica Intermediate | 241 | 87.60% | 2.50% | 4.98% | 4.98% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 0.00% | 5.56% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318608583 | C -> A | LOC_Os03g32526.1 | missense_variant ; p.Val40Phe; MODERATE | nonsynonymous_codon ; V40F | Average:31.562; most accessible tissue: Minghui63 young leaf, score: 63.571 | benign  |
0.107 |
TOLERATED | 1.00 |
| vg0318608583 | C -> DEL | LOC_Os03g32526.1 | N | frameshift_variant | Average:31.562; most accessible tissue: Minghui63 young leaf, score: 63.571 | N | N | N | N |