Search for Variation information by Variation ID:
Detailed information for vg0430654100:
| Variant ID: vg0430654100 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30654100 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 404. )
Flanking Sequence (100 bp) in Reference Genome:
GTCGGCCAATAGAACCCTTGACGAAAGGCCTTGCCAACCAAGGTGCGCGAGGCGGAATGGGCTCCGCACTCGCCTTCATGGATATCGGCAAGAAGCTCAA[C/T]
GCCTTGTTCCTGAGGAATGCACTTCAGGAGGATTCCGTTAGCCGCGCGCCGATAGAGGGTCCCTTCTATCAGCACGTAGCGTTTGGAAATGCGTTGGACG
Reverse complement sequence
CGTCCAACGCATTTCCAAACGCTACGTGCTGATAGAAGGGACCCTCTATCGGCGCGCGGCTAACGGAATCCTCCTGAAGTGCATTCCTCAGGAACAAGGC[G/A]
TTGAGCTTCTTGCCGATATCCATGAAGGCGAGTGCGGAGCCCATTCCGCCTCGCGCACCTTGGTTGGCAAGGCCTTTCGTCAAGGGTTCTATTGGCCGAC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.60% | 0.10% | 0.38% | 14.92% | NA |
| All Indica | 2759 | 99.20% | 0.10% | 0.07% | 0.62% | NA |
| All Japonica | 1512 | 56.50% | 0.00% | 1.06% | 42.46% | NA |
| Aus | 269 | 92.60% | 0.00% | 0.00% | 7.43% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.00% | 0.17% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.00% | 0.43% | NA |
| Indica III | 913 | 99.50% | 0.30% | 0.11% | 0.11% | NA |
| Indica Intermediate | 786 | 98.20% | 0.00% | 0.13% | 1.65% | NA |
| Temperate Japonica | 767 | 65.70% | 0.00% | 0.26% | 34.03% | NA |
| Tropical Japonica | 504 | 46.20% | 0.00% | 1.98% | 51.79% | NA |
| Japonica Intermediate | 241 | 48.50% | 0.00% | 1.66% | 49.79% | NA |
| VI/Aromatic | 96 | 81.20% | 0.00% | 0.00% | 18.75% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 0.00% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430654100 | C -> DEL | LOC_Os04g51730.1 | N | frameshift_variant | Average:9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 | N | N | N | N |
| vg0430654100 | C -> T | LOC_Os04g51730.1 | missense_variant ; p.Val88Ile; MODERATE | nonsynonymous_codon ; V88I | Average:9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 | benign  |
0.409 |
DELETERIOUS | 0.03 |