Search for Variation information by Variation ID:
Detailed information for vg0118270489:
| Variant ID: vg0118270489 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 18270489 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 272. )
Flanking Sequence (100 bp) in Reference Genome:
GATTACTACGCACTGGTTTGAGGACCAGCGAACGTGTAGAATTATCTCTCGGACACCAATGGAGGTTGCGGTACGAGAGATTGCTACGCACTGGTTCGAG[G/A]
ACCAGCGAGCGAGTAGAATCATCTCTCAAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCAAGTAGAATCAT
Reverse complement sequence
ATGATTCTACTTGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCTCCATTGGTGTTTGAGAGATGATTCTACTCGCTCGCTGGT[C/T]
CTCGAACCAGTGCGTAGCAATCTCTCGTACCGCAACCTCCATTGGTGTCCGAGAGATAATTCTACACGTTCGCTGGTCCTCAAACCAGTGCGTAGTAATC
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 | 97.90% | 0.20% | 1.97% | 0.00% | NA |
| All Indica | 2759 | 97.30% | 0.30% | 2.46% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 90.70% | 0.00% | 9.29% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 89.50% | 1.10% | 9.46% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.00% | 0.55% | 0.00% | NA |
| Indica Intermediate | 786 | 97.30% | 0.30% | 2.42% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0118270489 | G -> A | LOC_Os01g33180.1 | missense_variant ; p.Asp15Asn; MODERATE | nonsynonymous_codon ; D15N | Average:53.456; most accessible tissue: Minghui63 young leaf, score: 75.479 | benign  |
0.407 |
TOLERATED | 1.00 |