Search for Variation information by Variation ID:
Detailed information for vg0139512862:
| Variant ID: vg0139512862 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39512862 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTGAGAACACACTCATGCTTCACTCTCTTGCGGTAGATACCCCTGCCTGCCTTATCTTGACATAGTATCTCAAACCTGTGCTGTTGGGTACCTTGCACTA[G/C]
AGCTCGATGTTTCATAGCCTTTTTACGCAACTCCTCTAGCTTTTTCTGCATGAAAGCTCCAAACAAAATGCTGTTGTTCGGCATAGAGGGAAGAACTGCC
Reverse complement sequence
GGCAGTTCTTCCCTCTATGCCGAACAACAGCATTTTGTTTGGAGCTTTCATGCAGAAAAAGCTAGAGGAGTTGCGTAAAAAGGCTATGAAACATCGAGCT[C/G]
TAGTGCAAGGTACCCAACAGCACAGGTTTGAGATACTATGTCAAGATAAGGCAGGCAGGGGTATCTACCGCAAGAGAGTGAAGCATGAGTGTGTTCTCAA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 26.20% | 0.10% | 1.84% | 71.84% | NA |
| All Indica | 2759 | 2.50% | 0.20% | 1.70% | 95.54% | NA |
| All Japonica | 1512 | 74.50% | 0.00% | 0.40% | 25.07% | NA |
| Aus | 269 | 0.40% | 0.00% | 2.23% | 97.40% | NA |
| Indica I | 595 | 3.50% | 0.00% | 0.50% | 95.97% | NA |
| Indica II | 465 | 1.50% | 1.30% | 1.08% | 96.13% | NA |
| Indica III | 913 | 1.20% | 0.00% | 1.20% | 97.59% | NA |
| Indica Intermediate | 786 | 3.90% | 0.00% | 3.56% | 92.49% | NA |
| Temperate Japonica | 767 | 97.30% | 0.00% | 0.00% | 2.74% | NA |
| Tropical Japonica | 504 | 52.40% | 0.00% | 0.60% | 47.02% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0139512862 | G -> DEL | LOC_Os01g67990.1 | N | frameshift_variant | Average:11.812; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg0139512862 | G -> C | LOC_Os01g67990.1 | missense_variant ; p.Leu678Val; MODERATE | nonsynonymous_codon ; L678V | Average:11.812; most accessible tissue: Zhenshan97 root, score: 16.934 | benign  |
0.343 |
TOLERATED | 1.00 |