Search for Variation information by Variation ID:
Detailed information for vg0300825998:
| Variant ID: vg0300825998 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 825998 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGAGCCCCCGACCCCCAGGAAGGCCCTGAGGCCACTGTGGGAAGGCCGCACCTATCGCCCTTTGACCCCGAGGCTAACCCTGTGCTGACTCGACCCGGGA[A/G]
AGAGCAGGGAGAAGAGGCCCCCGAGCCGAACGGAGGCCTAAGGCCCCTGACGACCGGAGTTGGCCCTTTGCCCGCTTGTCCGACGACGCCAGGAGCCCCC
Reverse complement sequence
GGGGGCTCCTGGCGTCGTCGGACAAGCGGGCAAAGGGCCAACTCCGGTCGTCAGGGGCCTTAGGCCTCCGTTCGGCTCGGGGGCCTCTTCTCCCTGCTCT[T/C]
TCCCGGGTCGAGTCAGCACAGGGTTAGCCTCGGGGTCAAAGGGCGATAGGTGCGGCCTTCCCACAGTGGCCTCAGGGCCTTCCTGGGGGTCGGGGGCTCC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 13.10% | 2.40% | 1.38% | 83.14% | NA |
| All Indica | 2759 | 1.10% | 3.40% | 2.03% | 93.48% | NA |
| All Japonica | 1512 | 37.40% | 0.10% | 0.53% | 61.97% | NA |
| Aus | 269 | 1.50% | 1.50% | 0.00% | 97.03% | NA |
| Indica I | 595 | 0.20% | 4.00% | 2.35% | 93.45% | NA |
| Indica II | 465 | 4.30% | 2.80% | 2.80% | 90.11% | NA |
| Indica III | 913 | 0.40% | 3.50% | 1.42% | 94.63% | NA |
| Indica Intermediate | 786 | 0.50% | 3.30% | 2.04% | 94.15% | NA |
| Temperate Japonica | 767 | 61.40% | 0.00% | 0.26% | 38.33% | NA |
| Tropical Japonica | 504 | 6.30% | 0.00% | 0.60% | 93.06% | NA |
| Japonica Intermediate | 241 | 26.10% | 0.40% | 1.24% | 72.20% | NA |
| VI/Aromatic | 96 | 5.20% | 13.50% | 0.00% | 81.25% | NA |
| Intermediate | 90 | 15.60% | 1.10% | 1.11% | 82.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0300825998 | A -> DEL | LOC_Os03g02350.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0300825998 | A -> G | LOC_Os03g02350.1 | missense_variant ; p.Lys1226Arg; MODERATE | nonsynonymous_codon ; K1226R | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.129 |
TOLERATED | 1.00 |