Search for Variation information by Variation ID:
Detailed information for vg0300825980:
| Variant ID: vg0300825980 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 825980 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCTTGTCAGACGGTGCTAGGAGCCCCCGACCCCCAGGAAGGCCCTGAGGCCACTGTGGGAAGGCCGCACCTATCGCCCTTTGACCCCGAGGCTAACCCTG[T/C]
GCTGACTCGACCCGGGAAAGAGCAGGGAGAAGAGGCCCCCGAGCCGAACGGAGGCCTAAGGCCCCTGACGACCGGAGTTGGCCCTTTGCCCGCTTGTCCG
Reverse complement sequence
CGGACAAGCGGGCAAAGGGCCAACTCCGGTCGTCAGGGGCCTTAGGCCTCCGTTCGGCTCGGGGGCCTCTTCTCCCTGCTCTTTCCCGGGTCGAGTCAGC[A/G]
CAGGGTTAGCCTCGGGGTCAAAGGGCGATAGGTGCGGCCTTCCCACAGTGGCCTCAGGGCCTTCCTGGGGGTCGGGGGCTCCTAGCACCGTCTGACAAGC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 15.90% | 1.00% | 2.39% | 80.66% | NA |
| All Indica | 2759 | 5.30% | 1.40% | 3.73% | 89.60% | NA |
| All Japonica | 1512 | 37.80% | 0.10% | 0.20% | 61.97% | NA |
| Aus | 269 | 4.10% | 0.00% | 0.37% | 95.54% | NA |
| Indica I | 595 | 2.40% | 3.50% | 3.36% | 90.76% | NA |
| Indica II | 465 | 7.10% | 1.70% | 6.88% | 84.30% | NA |
| Indica III | 913 | 6.90% | 0.10% | 2.19% | 90.80% | NA |
| Indica Intermediate | 786 | 4.60% | 1.00% | 3.94% | 90.46% | NA |
| Temperate Japonica | 767 | 61.40% | 0.00% | 0.26% | 38.33% | NA |
| Tropical Japonica | 504 | 7.10% | 0.00% | 0.20% | 92.66% | NA |
| Japonica Intermediate | 241 | 26.60% | 0.40% | 0.00% | 73.03% | NA |
| VI/Aromatic | 96 | 7.30% | 9.40% | 2.08% | 81.25% | NA |
| Intermediate | 90 | 18.90% | 1.10% | 4.44% | 75.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0300825980 | T -> C | LOC_Os03g02350.1 | missense_variant ; p.Val1220Ala; MODERATE | nonsynonymous_codon ; V1220A | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.134 |
DELETERIOUS | 0.00 |
| vg0300825980 | T -> DEL | LOC_Os03g02350.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |