Search for Variation information by Variation ID:
Detailed information for vg0509254430:
| Variant ID: vg0509254430 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 9254430 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATGTACGACATTTACACTTAGCATACATGACTTAGATTGTTAAAACATAAATGTCTCGTGACTTAGCAGATGTTTCTTGTATCAACAGATGGCTGACCGC[G/A]
ATGAGGAACAGATATTGTACGATACAATCGCGGAGGGAAGCAGCCAGTACTGGAATGAAGAAGAGGGGAACGAGGATCCAAACCAGTACTTGAACGAGGA
Reverse complement sequence
TCCTCGTTCAAGTACTGGTTTGGATCCTCGTTCCCCTCTTCTTCATTCCAGTACTGGCTGCTTCCCTCCGCGATTGTATCGTACAATATCTGTTCCTCAT[C/T]
GCGGTCAGCCATCTGTTGATACAAGAAACATCTGCTAAGTCACGAGACATTTATGTTTTAACAATCTAAGTCATGTATGCTAAGTGTAAATGTCGTACAT
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 | 90.00% | 0.30% | 2.98% | 6.67% | NA |
| All Indica | 2759 | 87.60% | 0.10% | 4.17% | 8.16% | NA |
| All Japonica | 1512 | 98.60% | 0.90% | 0.46% | 0.07% | NA |
| Aus | 269 | 62.50% | 0.00% | 6.69% | 30.86% | NA |
| Indica I | 595 | 93.10% | 0.20% | 1.34% | 5.38% | NA |
| Indica II | 465 | 76.60% | 0.00% | 6.02% | 17.42% | NA |
| Indica III | 913 | 86.50% | 0.00% | 5.91% | 7.56% | NA |
| Indica Intermediate | 786 | 91.20% | 0.10% | 3.18% | 5.47% | NA |
| Temperate Japonica | 767 | 98.40% | 1.20% | 0.26% | 0.13% | NA |
| Tropical Japonica | 504 | 99.00% | 0.40% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.80% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 93.30% | 1.10% | 0.00% | 5.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0509254430 | G -> DEL | LOC_Os05g16340.1 | N | frameshift_variant | Average:28.285; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |
| vg0509254430 | G -> A | LOC_Os05g16340.1 | missense_variant ; p.Asp116Asn; MODERATE | nonsynonymous_codon ; D116N | Average:28.285; most accessible tissue: Zhenshan97 panicle, score: 49.416 | benign  |
1.455 |
DELETERIOUS | 0.05 |