Search for Variation information by Variation ID:
Detailed information for vg0141808872:
| Variant ID: vg0141808872 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 41808872 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCCCCTCCCGGGGTAGATTGTTCCCCCCTGCGGCTCCCGCCCGCGCCATCGTGGCCTCGAGGAGCCCGCTCCTCCGACGCCCCGACCGCCTGCATGATGG[T/C]
CAGGATGGAGGCGCGGTCTGGATCGCTGCAGAGGGGGAGGACTCCTTGAGGAATGAGGGATGCGTCCACGGAGCTGAGATTCAGCACCCGTTGGACCACT
Reverse complement sequence
AGTGGTCCAACGGGTGCTGAATCTCAGCTCCGTGGACGCATCCCTCATTCCTCAAGGAGTCCTCCCCCTCTGCAGCGATCCAGACCGCGCCTCCATCCTG[A/G]
CCATCATGCAGGCGGTCGGGGCGTCGGAGGAGCGGGCTCCTCGAGGCCACGATGGCGCGGGCGGGAGCCGCAGGGGGGAACAATCTACCCCGGGAGGGGG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.80% | 0.10% | 4.97% | 67.10% | NA |
| All Indica | 2759 | 18.10% | 0.30% | 7.10% | 74.56% | NA |
| All Japonica | 1512 | 44.40% | 0.00% | 1.06% | 54.56% | NA |
| Aus | 269 | 37.20% | 0.00% | 5.58% | 57.25% | NA |
| Indica I | 595 | 12.30% | 0.50% | 8.40% | 78.82% | NA |
| Indica II | 465 | 12.00% | 0.20% | 2.80% | 84.95% | NA |
| Indica III | 913 | 26.50% | 0.30% | 7.01% | 66.16% | NA |
| Indica Intermediate | 786 | 16.30% | 0.00% | 8.78% | 74.94% | NA |
| Temperate Japonica | 767 | 77.20% | 0.00% | 0.39% | 22.43% | NA |
| Tropical Japonica | 504 | 5.60% | 0.00% | 1.98% | 92.46% | NA |
| Japonica Intermediate | 241 | 21.20% | 0.00% | 1.24% | 77.59% | NA |
| VI/Aromatic | 96 | 15.60% | 0.00% | 2.08% | 82.29% | NA |
| Intermediate | 90 | 31.10% | 0.00% | 6.67% | 62.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0141808872 | T -> DEL | LOC_Os01g72070.1 | N | frameshift_variant | Average:4.998; most accessible tissue: Callus, score: 10.303 | N | N | N | N |
| vg0141808872 | T -> C | LOC_Os01g72070.1 | missense_variant ; p.Thr234Ala; MODERATE | nonsynonymous_codon ; T234A | Average:4.998; most accessible tissue: Callus, score: 10.303 | benign  |
1.326 |
DELETERIOUS | 0.03 |