Search for Variation information by Variation ID:
Detailed information for vg0202706398:
| Variant ID: vg0202706398 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 2706398 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTGTTCGATAGGTATGTAGTCCGGATCATCATCGCGGGGGGCGACTTGTGTTATTTCCATTGGAAACGGGTCACTTGGTGTGCGCCACGTTTCTTCACTA[G/C]
AAGCGTCTGGCTGCTTATTGCTACCGGAATTTTGAGGAGCGTTACCTTCTTGAGGCGCTATTGGTGTGTTCGATGGAACCTTTTCGTTCGACATCTTCCA
Reverse complement sequence
TGGAAGATGTCGAACGAAAAGGTTCCATCGAACACACCAATAGCGCCTCAAGAAGGTAACGCTCCTCAAAATTCCGGTAGCAATAAGCAGCCAGACGCTT[C/G]
TAGTGAAGAAACGTGGCGCACACCAAGTGACCCGTTTCCAATGGAAATAACACAAGTCGCCCCCCGCGATGATGATCCGGACTACATACCTATCGAACAG
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 | 34.90% | 0.70% | 0.89% | 63.56% | NA |
| All Indica | 2759 | 8.20% | 0.90% | 1.20% | 89.74% | NA |
| All Japonica | 1512 | 87.20% | 0.00% | 0.20% | 12.57% | NA |
| Aus | 269 | 20.10% | 2.20% | 1.49% | 76.21% | NA |
| Indica I | 595 | 12.10% | 0.70% | 0.50% | 86.72% | NA |
| Indica II | 465 | 3.40% | 0.60% | 1.08% | 94.84% | NA |
| Indica III | 913 | 9.40% | 1.00% | 1.10% | 88.50% | NA |
| Indica Intermediate | 786 | 6.50% | 1.10% | 1.91% | 90.46% | NA |
| Temperate Japonica | 767 | 82.00% | 0.00% | 0.13% | 17.86% | NA |
| Tropical Japonica | 504 | 98.20% | 0.00% | 0.20% | 1.59% | NA |
| Japonica Intermediate | 241 | 80.90% | 0.00% | 0.41% | 18.67% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 1.04% | 97.92% | NA |
| Intermediate | 90 | 55.60% | 0.00% | 1.11% | 43.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0202706398 | G -> DEL | LOC_Os02g05570.1 | N | frameshift_variant | Average:5.325; most accessible tissue: Minghui63 flag leaf, score: 10.316 | N | N | N | N |
| vg0202706398 | G -> C | LOC_Os02g05570.1 | missense_variant ; p.Ser32Cys; MODERATE | nonsynonymous_codon ; S32C | Average:5.325; most accessible tissue: Minghui63 flag leaf, score: 10.316 | benign  |
0.49 |
DELETERIOUS | 0.03 |