Search for Variation information by Variation ID:
Detailed information for vg0409586716:
| Variant ID: vg0409586716 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9586716 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 250. )
Flanking Sequence (100 bp) in Reference Genome:
TTGTTCCTGTGATTCTGGCCACACGAGATAGAATTCAGAGAAGAGGCTGGATCCGTTAGAAAGAGGGCTCCGAGAGCTTTCCATCAAGTACTCACGGGCC[A/G]
AAAACGGAGGTCGTATGCAGATTCGGTGGCCGTTTGAAGTCAGCAGTGTAGTAGGTGGCCGAATCGGATTCCAGCACTTGGAGTACTTGATCTCGATATC
Reverse complement sequence
GATATCGAGATCAAGTACTCCAAGTGCTGGAATCCGATTCGGCCACCTACTACACTGCTGACTTCAAACGGCCACCGAATCTGCATACGACCTCCGTTTT[T/C]
GGCCCGTGAGTACTTGATGGAAAGCTCTCGGAGCCCTCTTTCTAACGGATCCAGCCTCTTCTCTGAATTCTATCTCGTGTGGCCAGAATCACAGGAACAA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.50% | 0.30% | 3.24% | 42.00% | NA |
| All Indica | 2759 | 38.40% | 0.00% | 4.60% | 56.98% | NA |
| All Japonica | 1512 | 84.10% | 0.80% | 0.40% | 14.75% | NA |
| Aus | 269 | 37.20% | 0.00% | 4.46% | 58.36% | NA |
| Indica I | 595 | 32.80% | 0.00% | 7.23% | 60.00% | NA |
| Indica II | 465 | 33.10% | 0.00% | 3.87% | 63.01% | NA |
| Indica III | 913 | 42.10% | 0.00% | 2.96% | 54.98% | NA |
| Indica Intermediate | 786 | 41.60% | 0.00% | 4.96% | 53.44% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 0.13% | 2.09% | NA |
| Tropical Japonica | 504 | 63.70% | 0.00% | 0.99% | 35.32% | NA |
| Japonica Intermediate | 241 | 83.00% | 5.00% | 0.00% | 12.03% | NA |
| VI/Aromatic | 96 | 83.30% | 0.00% | 6.25% | 10.42% | NA |
| Intermediate | 90 | 72.20% | 0.00% | 2.22% | 25.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409586716 | A -> DEL | LOC_Os04g17520.1 | N | frameshift_variant | Average:16.014; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |
| vg0409586716 | A -> G | LOC_Os04g17520.1 | missense_variant ; p.Leu50Ser; MODERATE | nonsynonymous_codon ; L50S | Average:16.014; most accessible tissue: Minghui63 root, score: 29.362 | possibly damaging  |
-1.521 |
TOLERATED | 0.18 |