Search for Variation information by Variation ID:
Detailed information for vg0722037460:
| Variant ID: vg0722037460 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 22037460 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 354. )
Flanking Sequence (100 bp) in Reference Genome:
CCTGACCCATTGTAGGTCTGCCATTTTCATCATCTTGGATACACCAGCAGGCAACCTTGCAAGCTTTTGTGAGCTCATCAGCACTGGCATCTCCATTCAA[C/A]
CTGGGGTCTAACAAGGTCTGCACATCACCTTCCTGGAGTTTGTTTACAGCCAAAGTTGGGAAGAAAGAGGACTTTCCCTCCTCCCCTAGATCAGCATTCC
Reverse complement sequence
GGAATGCTGATCTAGGGGAGGAGGGAAAGTCCTCTTTCTTCCCAACTTTGGCTGTAAACAAACTCCAGGAAGGTGATGTGCAGACCTTGTTAGACCCCAG[G/T]
TTGAATGGAGATGCCAGTGCTGATGAGCTCACAAAAGCTTGCAAGGTTGCCTGCTGGTGTATCCAAGATGATGAAAATGGCAGACCTACAATGGGTCAGG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.80% | 0.20% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.30% | 0.60% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.90% | 3.70% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0722037460 | C -> A | LOC_Os07g36780.1 | missense_variant ; p.Arg725Ser; MODERATE | nonsynonymous_codon ; R725S | Average:71.166; most accessible tissue: Callus, score: 88.307 | benign  |
0.896 |
TOLERATED | 0.20 |