Search for Variation information by Variation ID:
Detailed information for vg0430654148:
| Variant ID: vg0430654148 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30654148 |
| 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, others allele: 0.00, population size: 363. )
Flanking Sequence (100 bp) in Reference Genome:
GAGGCGGAATGGGCTCCGCACTCGCCTTCATGGATATCGGCAAGAAGCTCAACGCCTTGTTCCTGAGGAATGCACTTCAGGAGGATTCCGTTAGCCGCGC[G/A]
CCGATAGAGGGTCCCTTCTATCAGCACGTAGCGTTTGGAAATGCGTTGGACGCGTTCTGTCACGCTCAGAAATTCCCGAATAGAATTCCAAGCAGAATGT
Reverse complement sequence
ACATTCTGCTTGGAATTCTATTCGGGAATTTCTGAGCGTGACAGAACGCGTCCAACGCATTTCCAAACGCTACGTGCTGATAGAAGGGACCCTCTATCGG[C/T]
GCGCGGCTAACGGAATCCTCCTGAAGTGCATTCCTCAGGAACAAGGCGTTGAGCTTCTTGCCGATATCCATGAAGGCGAGTGCGGAGCCCATTCCGCCTC
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 | 76.00% | 0.00% | 7.13% | 16.80% | NA |
| All Indica | 2759 | 97.80% | 0.00% | 1.41% | 0.80% | NA |
| All Japonica | 1512 | 41.70% | 0.00% | 12.57% | 45.77% | NA |
| Aus | 269 | 56.50% | 0.40% | 24.16% | 18.96% | NA |
| Indica I | 595 | 99.50% | 0.00% | 0.34% | 0.17% | NA |
| Indica II | 465 | 97.20% | 0.00% | 2.15% | 0.65% | NA |
| Indica III | 913 | 99.20% | 0.00% | 0.66% | 0.11% | NA |
| Indica Intermediate | 786 | 95.20% | 0.00% | 2.67% | 2.16% | NA |
| Temperate Japonica | 767 | 64.70% | 0.00% | 0.65% | 34.68% | NA |
| Tropical Japonica | 504 | 12.70% | 0.00% | 28.57% | 58.73% | NA |
| Japonica Intermediate | 241 | 29.00% | 0.00% | 17.01% | 53.94% | NA |
| VI/Aromatic | 96 | 53.10% | 0.00% | 26.04% | 20.83% | NA |
| Intermediate | 90 | 70.00% | 0.00% | 20.00% | 10.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430654148 | G -> DEL | LOC_Os04g51730.1 | N | frameshift_variant | Average:9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 | N | N | N | N |
| vg0430654148 | G -> A | LOC_Os04g51730.1 | missense_variant ; p.Arg72Cys; MODERATE | nonsynonymous_codon ; R72C | Average:9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 | benign  |
0.919 |
DELETERIOUS | 0.01 |