Search for Variation information by Variation ID:
Detailed information for vg0727002951:
| Variant ID: vg0727002951 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 27002951 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 377. )
Flanking Sequence (100 bp) in Reference Genome:
ACAGAGGTTGTAGGCTGTAAAAGTTTCCGAGTCCTCGATCGTATATTTTGGTCACCTGCACCGTGCGTACTGGCCTTTACATACTGTCGTCCTGTGCTTT[G/C]
CATCAAGGGCACTTCACTATGTGGGAAATACCAACCACTTCTGTTAACTGCTCTAGCATTAGATGCTAATGATAACTTGATTCCAGTAGCATTTGCCATC
Reverse complement sequence
GATGGCAAATGCTACTGGAATCAAGTTATCATTAGCATCTAATGCTAGAGCAGTTAACAGAAGTGGTTGGTATTTCCCACATAGTGAAGTGCCCTTGATG[C/G]
AAAGCACAGGACGACAGTATGTAAAGGCCAGTACGCACGGTGCAGGTGACCAAAATATACGATCGAGGACTCGGAAACTTTTACAGCCTACAACCTCTGT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.60% | 0.30% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 93.70% | 4.80% | 1.49% | 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 | 100.00% | 0.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0727002951 | G -> C | LOC_Os07g45250.1 | missense_variant ; p.Cys296Ser; MODERATE | nonsynonymous_codon ; C296S | Average:58.12; most accessible tissue: Callus, score: 85.205 | benign  |
1.467 |
DELETERIOUS | 0.01 |