Search for Variation information by Variation ID:
Detailed information for vg0625552984:
| Variant ID: vg0625552984 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 25552984 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 111. )
Flanking Sequence (100 bp) in Reference Genome:
TTTTCTGGACTTCGAGGCTTGAATGGTCTCTTGACTTCTGATGCAACGTAAGCGTCGAGCTCCTCTTGCGTGCAATCGTACCCCGGGTCCTTGTTCTTGG[C/A]
GGCGTCAACTTTCGCCTTCTTCGTTGCCCTTGTGTGGGTAGGCGGTGGAGCTGGGGGGGCCCTTGACTTTGAAGGTGCCGGAAGAGGAGCTTGCGGGGGA
Reverse complement sequence
TCCCCCGCAAGCTCCTCTTCCGGCACCTTCAAAGTCAAGGGCCCCCCCAGCTCCACCGCCTACCCACACAAGGGCAACGAAGAAGGCGAAAGTTGACGCC[G/T]
CCAAGAACAAGGACCCGGGGTACGATTGCACGCAAGAGGAGCTCGACGCTTACGTTGCATCAGAAGTCAAGAGACCATTCAAGCCTCGAAGTCCAGAAAA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 12.70% | 0.10% | 4.49% | 82.71% | NA |
| All Indica | 2759 | 0.80% | 0.30% | 5.44% | 93.55% | NA |
| All Japonica | 1512 | 37.60% | 0.00% | 0.07% | 62.30% | NA |
| Aus | 269 | 0.40% | 0.00% | 16.73% | 82.90% | NA |
| Indica I | 595 | 0.30% | 0.30% | 2.18% | 97.14% | NA |
| Indica II | 465 | 0.60% | 0.20% | 3.01% | 96.13% | NA |
| Indica III | 913 | 0.70% | 0.40% | 7.78% | 91.13% | NA |
| Indica Intermediate | 786 | 1.30% | 0.00% | 6.62% | 92.11% | NA |
| Temperate Japonica | 767 | 62.80% | 0.00% | 0.00% | 37.16% | NA |
| Tropical Japonica | 504 | 2.60% | 0.00% | 0.00% | 97.42% | NA |
| Japonica Intermediate | 241 | 30.70% | 0.00% | 0.41% | 68.88% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 15.62% | 84.38% | NA |
| Intermediate | 90 | 7.80% | 0.00% | 1.11% | 91.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0625552984 | C -> A | LOC_Os06g42500.1 | missense_variant ; p.Ala596Ser; MODERATE | nonsynonymous_codon ; A596S | Average:7.911; most accessible tissue: Zhenshan97 flower, score: 13.891 | benign  |
0.351 |
DELETERIOUS | 0.01 |
| vg0625552984 | C -> DEL | LOC_Os06g42500.1 | N | frameshift_variant | Average:7.911; most accessible tissue: Zhenshan97 flower, score: 13.891 | N | N | N | N |