Search for Variation information by Variation ID:
Detailed information for vg0908137199:
| Variant ID: vg0908137199 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 8137199 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGTGTGTTTTTCTAAGCTCTCGCATTCTTTCGTGTGCGCCAAGCTTTTCCTGTTCAGCCCAATGGCCGAACAAGCAAAGGCGCACAACCTCTCTCCGAGT[G/A]
TTAGCGGTGACGACGGGGAGCCGAACCCACGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAAAGTCCTAGGCGGGAGGAGGCGCTCGAGAGGGT
Reverse complement sequence
ACCCTCTCGAGCGCCTCCTCCCGCCTAGGACTTTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCGTGGGTTCGGCTCCCCGTCGTCACCGCTAA[C/T]
ACTCGGAGAGAGGTTGTGCGCCTTTGCTTGTTCGGCCATTGGGCTGAACAGGAAAAGCTTGGCGCACACGAAAGAATGCGAGAGCTTAGAAAAACACACG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 53.10% | 0.10% | 7.89% | 38.85% | NA |
| All Indica | 2759 | 35.80% | 0.00% | 5.40% | 58.75% | NA |
| All Japonica | 1512 | 85.10% | 0.00% | 10.12% | 4.83% | NA |
| Aus | 269 | 33.80% | 0.00% | 23.42% | 42.75% | NA |
| Indica I | 595 | 13.60% | 0.00% | 7.23% | 79.16% | NA |
| Indica II | 465 | 68.60% | 0.00% | 2.37% | 29.03% | NA |
| Indica III | 913 | 32.30% | 0.00% | 5.81% | 61.88% | NA |
| Indica Intermediate | 786 | 37.40% | 0.00% | 5.34% | 57.25% | NA |
| Temperate Japonica | 767 | 91.70% | 0.00% | 6.91% | 1.43% | NA |
| Tropical Japonica | 504 | 81.50% | 0.00% | 11.31% | 7.14% | NA |
| Japonica Intermediate | 241 | 71.40% | 0.00% | 17.84% | 10.79% | NA |
| VI/Aromatic | 96 | 81.20% | 6.20% | 4.17% | 8.33% | NA |
| Intermediate | 90 | 74.40% | 0.00% | 4.44% | 21.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0908137199 | G -> DEL | LOC_Os09g13850.1 | N | frameshift_variant | Average:20.001; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0908137199 | G -> A | LOC_Os09g13850.1 | missense_variant ; p.Val14Ile; MODERATE | nonsynonymous_codon ; V14I | Average:20.001; most accessible tissue: Minghui63 panicle, score: 46.754 | benign  |
0.171 |
DELETERIOUS | 0.04 |