Search for Variation information by Variation ID:
Detailed information for vg0118270711:
| Variant ID: vg0118270711 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 18270711 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 318. )
Flanking Sequence (100 bp) in Reference Genome:
TGCGGTGCGGGAGATTGCTACGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATG[G/A]
AGGTTGTGGTGTAGGAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACGAATGAAAGTGCTAGAGTTGGTTTATTA
Reverse complement sequence
TAATAAACCAACTCTAGCACTTTCATTCGTGTTCGAGAGATGATTCTACTCGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTCCTACACCACAACCT[C/T]
CATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTGGTTCTTGAACCAGTACGTAGCAATCTCCCGCACCGCA
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 | 98.50% | 1.20% | 0.32% | 0.00% | NA |
| All Indica | 2759 | 97.60% | 2.10% | 0.36% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.10% | 0.00% | 1.86% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 89.70% | 10.10% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.00% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 98.10% | 1.30% | 0.64% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0118270711 | G -> A | LOC_Os01g33180.1 | missense_variant ; p.Glu89Lys; MODERATE | nonsynonymous_codon ; E89K | Average:54.099; most accessible tissue: Minghui63 young leaf, score: 70.038 | benign  |
0.481 |
TOLERATED | 0.17 |