Search for Variation information by Variation ID:
Detailed information for vg0910657672:
| Variant ID: vg0910657672 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10657672 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTCACCAACGCGGGCCTCCCCAGGACCGCGTTGTAGGGCAGACTGAGGTCCGCCACATCGAAGTCCACCCGCTCCGTGCGGAAGTTGGCGGAATCACCGA[T/A]
GGTGACCGGGAGGTCGATATGACCCAGCGGCCAGGTGTGCCCCGGCGTCACACCGATGATCGGCTGGGACGGCCGGAGCACCATCCCTGGGGCCTTGATG
Reverse complement sequence
CATCAAGGCCCCAGGGATGGTGCTCCGGCCGTCCCAGCCGATCATCGGTGTGACGCCGGGGCACACCTGGCCGCTGGGTCATATCGACCTCCCGGTCACC[A/T]
TCGGTGATTCCGCCAACTTCCGCACGGAGCGGGTGGACTTCGATGTGGCGGACCTCAGTCTGCCCTACAACGCGGTCCTGGGGAGGCCCGCGTTGGTGAA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 38.00% | 0.60% | 13.22% | 48.14% | NA |
| All Indica | 2759 | 29.10% | 0.20% | 19.64% | 51.03% | NA |
| All Japonica | 1512 | 54.70% | 1.60% | 0.93% | 42.79% | NA |
| Aus | 269 | 36.40% | 0.00% | 22.68% | 40.89% | NA |
| Indica I | 595 | 42.70% | 0.30% | 9.92% | 47.06% | NA |
| Indica II | 465 | 22.40% | 0.00% | 12.90% | 64.73% | NA |
| Indica III | 913 | 22.10% | 0.10% | 31.87% | 45.89% | NA |
| Indica Intermediate | 786 | 30.90% | 0.40% | 16.79% | 51.91% | NA |
| Temperate Japonica | 767 | 76.90% | 0.10% | 0.39% | 22.56% | NA |
| Tropical Japonica | 504 | 27.00% | 4.60% | 1.59% | 66.87% | NA |
| Japonica Intermediate | 241 | 41.90% | 0.00% | 1.24% | 56.85% | NA |
| VI/Aromatic | 96 | 32.30% | 0.00% | 4.17% | 63.54% | NA |
| Intermediate | 90 | 41.10% | 0.00% | 4.44% | 54.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910657672 | T -> DEL | LOC_Os09g17420.1 | N | frameshift_variant | Average:10.919; most accessible tissue: Callus, score: 20.752 | N | N | N | N |
| vg0910657672 | T -> A | LOC_Os09g17420.1 | missense_variant ; p.Ile67Phe; MODERATE | nonsynonymous_codon ; I67F | Average:10.919; most accessible tissue: Callus, score: 20.752 | possibly damaging  |
-1.871 |
TOLERATED | 1.00 |