Search for Variation information by Variation ID:
Detailed information for vg0318608574:
| Variant ID: vg0318608574 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18608574 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCCAAGCCGCCATATAGAAAAAAAATTCAAAGGTGGTGCCGGTGATTGCAAAGCGAGCGCTCGGGGCGGGGCGGGGAGGGGCGTACCTTGGAGTCCGCGA[C/T]
GAGGCGGACGTAGTCCCAGCTGAGGACGATCTTGTGGAAGCGGTCCATGGTGGAGGCGGCGACGCCCGACGAGGAGGAGGAGGCGCCGCCTCCGCCTCCG
Reverse complement sequence
CGGAGGCGGAGGCGGCGCCTCCTCCTCCTCGTCGGGCGTCGCCGCCTCCACCATGGACCGCTTCCACAAGATCGTCCTCAGCTGGGACTACGTCCGCCTC[G/A]
TCGCGGACTCCAAGGTACGCCCCTCCCCGCCCCGCCCCGAGCGCTCGCTTTGCAATCACCGGCACCACCTTTGAATTTTTTTTCTATATGGCGGCTTGGG
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 | 58.30% | 0.60% | 20.84% | 20.31% | NA |
| All Indica | 2759 | 40.90% | 0.90% | 29.47% | 28.71% | NA |
| All Japonica | 1512 | 88.10% | 0.00% | 2.38% | 9.52% | NA |
| Aus | 269 | 50.90% | 0.40% | 45.72% | 2.97% | NA |
| Indica I | 595 | 40.00% | 0.00% | 17.65% | 42.35% | NA |
| Indica II | 465 | 30.30% | 0.00% | 52.04% | 17.63% | NA |
| Indica III | 913 | 47.90% | 2.20% | 26.73% | 23.22% | NA |
| Indica Intermediate | 786 | 39.80% | 0.60% | 28.24% | 31.30% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 69.80% | 0.00% | 5.95% | 24.21% | NA |
| Japonica Intermediate | 241 | 89.20% | 0.00% | 2.07% | 8.71% | NA |
| VI/Aromatic | 96 | 96.90% | 1.00% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 70.00% | 0.00% | 12.22% | 17.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318608574 | C -> T | LOC_Os03g32526.1 | missense_variant ; p.Val43Ile; MODERATE | nonsynonymous_codon ; V43I | Average:31.686; most accessible tissue: Minghui63 young leaf, score: 63.571 | benign  |
0.95 |
TOLERATED | 0.15 |
| vg0318608574 | C -> DEL | LOC_Os03g32526.1 | N | frameshift_variant | Average:31.686; most accessible tissue: Minghui63 young leaf, score: 63.571 | N | N | N | N |