Search for Variation information by Variation ID:
Detailed information for vg0908138309:
| Variant ID: vg0908138309 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 8138309 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CATCCCTGCACACGCGGTGATCTACGCGTTCAGGGGGGGTGTGCGGCACAACCGCGTGCTCGAAAAGATCGCCTCCAAGGAGCCCCAGACTACCGCGGAG[C/G]
TTTTTCAGCTCGCGGACCGAGTGGCTCGCAAGGAGGAGGCCTGGACTTGGAACCCCTCCGGTTCCGGTGTGGCAGCTTCGGCCGCCCCCGGGTCCGCCGC
Reverse complement sequence
GCGGCGGACCCGGGGGCGGCCGAAGCTGCCACACCGGAACCGGAGGGGTTCCAAGTCCAGGCCTCCTCCTTGCGAGCCACTCGGTCCGCGAGCTGAAAAA[G/C]
CTCCGCGGTAGTCTGGGGCTCCTTGGAGGCGATCTTTTCGAGCACGCGGTTGTGCCGCACACCCCCCCTGAACGCGTAGATCACCGCGTGTGCAGGGATG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.80% | 1.40% | 17.46% | 40.39% | NA |
| All Indica | 2759 | 36.50% | 0.00% | 19.43% | 44.04% | NA |
| All Japonica | 1512 | 49.90% | 4.20% | 13.43% | 32.47% | NA |
| Aus | 269 | 10.40% | 0.00% | 25.28% | 64.31% | NA |
| Indica I | 595 | 14.50% | 0.00% | 16.30% | 69.24% | NA |
| Indica II | 465 | 68.00% | 0.00% | 7.53% | 24.52% | NA |
| Indica III | 913 | 34.60% | 0.00% | 30.01% | 35.38% | NA |
| Indica Intermediate | 786 | 36.90% | 0.00% | 16.54% | 46.56% | NA |
| Temperate Japonica | 767 | 72.50% | 8.20% | 13.43% | 5.87% | NA |
| Tropical Japonica | 504 | 24.40% | 0.00% | 14.09% | 61.51% | NA |
| Japonica Intermediate | 241 | 31.10% | 0.40% | 12.03% | 56.43% | NA |
| VI/Aromatic | 96 | 85.40% | 0.00% | 4.17% | 10.42% | NA |
| Intermediate | 90 | 62.20% | 0.00% | 15.56% | 22.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0908138309 | C -> G | LOC_Os09g13850.1 | missense_variant ; p.Leu384Val; MODERATE | nonsynonymous_codon ; L384V | Average:28.07; most accessible tissue: Minghui63 panicle, score: 66.554 | benign  |
0.523 |
DELETERIOUS | 0.01 |
| vg0908138309 | C -> DEL | LOC_Os09g13850.1 | N | frameshift_variant | Average:28.07; most accessible tissue: Minghui63 panicle, score: 66.554 | N | N | N | N |