Search for Variation information by Variation ID:
Detailed information for vg0625554535:
| Variant ID: vg0625554535 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 25554535 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 300. )
Flanking Sequence (100 bp) in Reference Genome:
TCAGAGTCCACCTTTTCACTTTGTCCTCTGTACCCGCAGGAAGGGTGAATGTCTCGAGCATTGTGGTCCACAGCATCTCTTTCTCCGAATCTGGGACAAA[G/T]
CTCTCATGATCTCCGTGTGCCCTTGTTCTTCGCCAGTACACCGTACTGACAGGCACGTTATCCCGCACAACCCAACCGCTGTGACGTACATAGTTCTTGG
Reverse complement sequence
CCAAGAACTATGTACGTCACAGCGGTTGGGTTGTGCGGGATAACGTGCCTGTCAGTACGGTGTACTGGCGAAGAACAAGGGCACACGGAGATCATGAGAG[C/A]
TTTGTCCCAGATTCGGAGAAAGAGATGCTGTGGACCACAATGCTCGAGACATTCACCCTTCCTGCGGGTACAGAGGACAAAGTGAAAAGGTGGACTCTGA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 7.00% | 2.70% | 18.66% | 71.65% | NA |
| All Indica | 2759 | 1.10% | 4.50% | 16.85% | 77.60% | NA |
| All Japonica | 1512 | 19.30% | 0.10% | 19.25% | 61.31% | NA |
| Aus | 269 | 0.00% | 0.00% | 31.97% | 68.03% | NA |
| Indica I | 595 | 0.30% | 5.20% | 8.40% | 86.05% | NA |
| Indica II | 465 | 1.90% | 3.00% | 14.62% | 80.43% | NA |
| Indica III | 913 | 0.70% | 4.20% | 22.89% | 72.29% | NA |
| Indica Intermediate | 786 | 1.50% | 5.20% | 17.56% | 75.70% | NA |
| Temperate Japonica | 767 | 32.60% | 0.10% | 25.81% | 41.46% | NA |
| Tropical Japonica | 504 | 2.60% | 0.20% | 7.54% | 89.68% | NA |
| Japonica Intermediate | 241 | 12.00% | 0.00% | 22.82% | 65.15% | NA |
| VI/Aromatic | 96 | 3.10% | 1.00% | 30.21% | 65.62% | NA |
| Intermediate | 90 | 6.70% | 1.10% | 12.22% | 80.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0625554535 | G -> T | LOC_Os06g42500.1 | missense_variant ; p.Ser142Arg; MODERATE | nonsynonymous_codon ; S142R | Average:14.143; most accessible tissue: Zhenshan97 panicle, score: 20.424 | benign  |
0.62 |
DELETERIOUS | 0.00 |
| vg0625554535 | G -> DEL | LOC_Os06g42500.1 | N | frameshift_variant | Average:14.143; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |