Search for Variation information by Variation ID:
Detailed information for vg0512023300:
| Variant ID: vg0512023300 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12023300 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGATCTCCACAGTTGAAACACACCACGGGCTTGTTGCCTTGCTCCCTCTTGGCAGGTTGTTGCTGTGCTGGAGCTGCAACAGGACGTGGAGCTTGATTAC[G/A]
GATGTTGTTGCCAGCATTGTTGTTGAAGAACTGACGCTGCGGACGAACAACAGACGAAGAACCTCCCTGTGGCATGGGCTGGGGTCCTAAAGTAAGACGC
Reverse complement sequence
GCGTCTTACTTTAGGACCCCAGCCCATGCCACAGGGAGGTTCTTCGTCTGTTGTTCGTCCGCAGCGTCAGTTCTTCAACAACAATGCTGGCAACAACATC[C/T]
GTAATCAAGCTCCACGTCCTGTTGCAGCTCCAGCACAGCAACAACCTGCCAAGAGGGAGCAAGGCAACAAGCCCGTGGTGTGTTTCAACTGTGGAGATCC
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 | 91.90% | 0.70% | 2.79% | 4.63% | NA |
| All Indica | 2759 | 91.00% | 0.90% | 4.06% | 3.99% | NA |
| All Japonica | 1512 | 99.70% | 0.10% | 0.00% | 0.20% | NA |
| Aus | 269 | 55.00% | 1.10% | 6.32% | 37.55% | NA |
| Indica I | 595 | 92.40% | 0.70% | 6.39% | 0.50% | NA |
| Indica II | 465 | 98.70% | 0.00% | 1.08% | 0.22% | NA |
| Indica III | 913 | 87.50% | 2.10% | 4.82% | 5.59% | NA |
| Indica Intermediate | 786 | 89.40% | 0.40% | 3.18% | 7.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.20% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 0.00% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512023300 | G -> DEL | LOC_Os05g20480.1 | N | frameshift_variant | Average:29.444; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 | N | N | N | N |
| vg0512023300 | G -> A | LOC_Os05g20480.1 | missense_variant ; p.Arg55Cys; MODERATE | nonsynonymous_codon ; R55C | Average:29.444; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 | probably damaging  |
2.729 |
DELETERIOUS | 0.01 |