Search for Variation information by Variation ID:
Detailed information for vg0118270643:
| Variant ID: vg0118270643 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 18270643 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 286. )
Flanking Sequence (100 bp) in Reference Genome:
GAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCAAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCA[A/T]
GAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGAGGTTGTGGTGTAGGAGATTGCTACGTACTGG
Reverse complement sequence
CCAGTACGTAGCAATCTCCTACACCACAACCTCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTGGTTC[T/A]
TGAACCAGTACGTAGCAATCTCCCGCACCGCAACCTCCATTGGTGTTCGAGAGATGATTCTACTTGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.70% | 1.00% | 1.31% | 0.00% | NA |
| All Indica | 2759 | 97.10% | 0.90% | 2.07% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 90.30% | 7.80% | 1.86% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 89.00% | 1.10% | 9.89% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.80% | 1.80% | 1.40% | 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 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0118270643 | A -> T | LOC_Os01g33180.1 | missense_variant ; p.Lys66Met; MODERATE | nonsynonymous_codon ; K66M | Average:52.848; most accessible tissue: Minghui63 young leaf, score: 70.655 | probably damaging  |
2.564 |
DELETERIOUS | 0.00 |