Search for Variation information by Variation ID:
Detailed information for vg0139512853:
| Variant ID: vg0139512853 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39512853 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCGTCGGCTTTGAGAACACACTCATGCTTCACTCTCTTGCGGTAGATACCCCTGCCTGCCTTATCTTGACATAGTATCTCAAACCTGTGCTGTTGGGTAC[C/A]
TTGCACTAGAGCTCGATGTTTCATAGCCTTTTTACGCAACTCCTCTAGCTTTTTCTGCATGAAAGCTCCAAACAAAATGCTGTTGTTCGGCATAGAGGGA
Reverse complement sequence
TCCCTCTATGCCGAACAACAGCATTTTGTTTGGAGCTTTCATGCAGAAAAAGCTAGAGGAGTTGCGTAAAAAGGCTATGAAACATCGAGCTCTAGTGCAA[G/T]
GTACCCAACAGCACAGGTTTGAGATACTATGTCAAGATAAGGCAGGCAGGGGTATCTACCGCAAGAGAGTGAAGCATGAGTGTGTTCTCAAAGCCGACGG
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 | 26.20% | 0.10% | 1.90% | 71.75% | NA |
| All Indica | 2759 | 2.60% | 0.20% | 1.78% | 95.36% | NA |
| All Japonica | 1512 | 74.50% | 0.00% | 0.40% | 25.13% | NA |
| Aus | 269 | 0.00% | 0.00% | 2.60% | 97.40% | NA |
| Indica I | 595 | 3.50% | 0.00% | 0.84% | 95.63% | NA |
| Indica II | 465 | 1.70% | 1.30% | 1.29% | 95.70% | NA |
| Indica III | 913 | 1.30% | 0.00% | 1.10% | 97.59% | NA |
| Indica Intermediate | 786 | 4.10% | 0.00% | 3.56% | 92.37% | NA |
| Temperate Japonica | 767 | 97.30% | 0.00% | 0.00% | 2.74% | NA |
| Tropical Japonica | 504 | 52.20% | 0.00% | 0.60% | 47.22% | NA |
| Japonica Intermediate | 241 | 48.50% | 0.00% | 1.24% | 50.21% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 22.92% | 75.00% | NA |
| Intermediate | 90 | 42.20% | 0.00% | 6.67% | 51.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139512853 | C -> A | LOC_Os01g67990.1 | missense_variant ; p.Gly681Cys; MODERATE | nonsynonymous_codon ; G681C | Average:11.966; most accessible tissue: Zhenshan97 root, score: 16.934 | benign  |
0.849 |
DELETERIOUS | 0.01 |
| vg0139512853 | C -> DEL | LOC_Os01g67990.1 | N | frameshift_variant | Average:11.966; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |