Search for Variation information by Variation ID:
Detailed information for vg0908137676:
| Variant ID: vg0908137676 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 8137676 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGTGTCGTCAAGGCGGAGGGCGCGGCGAGCGACGGCTATTGCTCGCCATTCGGCCGCCACTCCTTCGTCAGCGCCTCCGACCCAGGAAGATCTGCGTGGG[G/A]
GGCCGGATGCCCGCATCAGTATCGAGCGCCGGCGTAATGGCCGACGTGCTGCCCACGCAACGGAGGGCGCCTCCTCGTCCGGAGTGTCACATCAACACGG
Reverse complement sequence
CCGTGTTGATGTGACACTCCGGACGAGGAGGCGCCCTCCGTTGCGTGGGCAGCACGTCGGCCATTACGCCGGCGCTCGATACTGATGCGGGCATCCGGCC[C/T]
CCCACGCAGATCTTCCTGGGTCGGAGGCGCTGACGAAGGAGTGGCGGCCGAATGGCGAGCAATAGCCGTCGCTCGCCGCGCCCTCCGCCTTGACGACACG
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 | 39.80% | 0.10% | 6.71% | 53.39% | NA |
| All Indica | 2759 | 33.00% | 0.00% | 6.85% | 60.13% | NA |
| All Japonica | 1512 | 55.60% | 0.30% | 2.31% | 41.73% | NA |
| Aus | 269 | 7.40% | 0.00% | 21.93% | 70.63% | NA |
| Indica I | 595 | 10.90% | 0.00% | 6.55% | 82.52% | NA |
| Indica II | 465 | 64.70% | 0.00% | 4.95% | 30.32% | NA |
| Indica III | 913 | 30.20% | 0.00% | 8.54% | 61.23% | NA |
| Indica Intermediate | 786 | 34.10% | 0.10% | 6.23% | 59.54% | NA |
| Temperate Japonica | 767 | 86.00% | 0.50% | 0.52% | 12.91% | NA |
| Tropical Japonica | 504 | 21.60% | 0.00% | 5.16% | 73.21% | NA |
| Japonica Intermediate | 241 | 29.90% | 0.40% | 2.07% | 67.63% | NA |
| VI/Aromatic | 96 | 60.40% | 0.00% | 25.00% | 14.58% | NA |
| Intermediate | 90 | 56.70% | 0.00% | 11.11% | 32.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0908137676 | G -> DEL | LOC_Os09g13850.1 | N | frameshift_variant | Average:26.256; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0908137676 | G -> A | LOC_Os09g13850.1 | missense_variant ; p.Gly173Arg; MODERATE | nonsynonymous_codon ; G173R | Average:26.256; most accessible tissue: Minghui63 panicle, score: 59.629 | probably damaging  |
2.134 |
DELETERIOUS | 0.05 |