Search for Variation information by Variation ID:
Detailed information for vg0135290219:
| Variant ID: vg0135290219 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 35290219 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGACAAGTTCACTAAGTGGCCCGAGGCTTATCCGGTTGTCAAGATCGATAAGCACTCTGCTCTTAAATTTATTAAGGGCATCACGGCCCGTTTTGGAGTG[C/A]
CTAACCGTATTATTACGGATAATGGCACCCAATTCACTAGTGAGCTCTTCGGCGACTACTGCGAAGACATGGGCATCAAGCTCTGCTTCGCCTCACCTGC
Reverse complement sequence
GCAGGTGAGGCGAAGCAGAGCTTGATGCCCATGTCTTCGCAGTAGTCGCCGAAGAGCTCACTAGTGAATTGGGTGCCATTATCCGTAATAATACGGTTAG[G/T]
CACTCCAAAACGGGCCGTGATGCCCTTAATAAATTTAAGAGCAGAGTGCTTATCGATCTTGACAACCGGATAAGCCTCGGGCCACTTAGTGAACTTGTCG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 26.40% | 0.20% | 4.93% | 68.47% | NA |
| All Indica | 2759 | 2.50% | 0.00% | 3.62% | 93.87% | NA |
| All Japonica | 1512 | 68.70% | 0.70% | 4.50% | 26.12% | NA |
| Aus | 269 | 1.50% | 0.00% | 23.05% | 75.46% | NA |
| Indica I | 595 | 4.20% | 0.00% | 0.50% | 95.29% | NA |
| Indica II | 465 | 0.60% | 0.00% | 0.86% | 98.49% | NA |
| Indica III | 913 | 0.80% | 0.00% | 7.34% | 91.89% | NA |
| Indica Intermediate | 786 | 4.30% | 0.00% | 3.31% | 92.37% | NA |
| Temperate Japonica | 767 | 66.60% | 0.00% | 3.13% | 30.25% | NA |
| Tropical Japonica | 504 | 66.90% | 0.80% | 5.56% | 26.79% | NA |
| Japonica Intermediate | 241 | 79.30% | 2.50% | 6.64% | 11.62% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 51.10% | 0.00% | 3.33% | 45.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0135290219 | C -> A | LOC_Os01g60990.1 | missense_variant ; p.Pro204Thr; MODERATE | nonsynonymous_codon ; P204T | Average:6.196; most accessible tissue: Zhenshan97 flag leaf, score: 17.069 | benign  |
0.666 |
DELETERIOUS | 0.00 |
| vg0135290219 | C -> DEL | LOC_Os01g60990.1 | N | frameshift_variant | Average:6.196; most accessible tissue: Zhenshan97 flag leaf, score: 17.069 | N | N | N | N |