Search for Variation information by Variation ID:
Detailed information for vg0700388228:
| Variant ID: vg0700388228 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 388228 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTCTTCACCGTGCAGTCGGTGTCACCGCCATCGGTGGTTGGCGGCTGCTACTTCCAGCCACGGGGGCCGGTGTTGAACCGCTACATCCCCTGCGTCCTCC[G/A]
CAAGAAGTGGGACGACTGGAAGAGCGACTGGTTCTACACCCCCCTCGCCGACGAAGCGCGCCTCCGACTTCCGAGCCAGCCCCCGGCGCAGGTCTCCAGC
Reverse complement sequence
GCTGGAGACCTGCGCCGGGGGCTGGCTCGGAAGTCGGAGGCGCGCTTCGTCGGCGAGGGGGGTGTAGAACCAGTCGCTCTTCCAGTCGTCCCACTTCTTG[C/T]
GGAGGACGCAGGGGATGTAGCGGTTCAACACCGGCCCCCGTGGCTGGAAGTAGCAGCCGCCAACCACCGATGGCGGTGACACCGACTGCACGGTGAAGAA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 41.80% | 0.40% | 3.00% | 54.78% | NA |
| All Indica | 2759 | 15.80% | 0.00% | 3.88% | 80.28% | NA |
| All Japonica | 1512 | 91.30% | 1.30% | 1.12% | 6.22% | NA |
| Aus | 269 | 3.70% | 0.00% | 5.95% | 90.33% | NA |
| Indica I | 595 | 5.70% | 0.00% | 3.03% | 91.26% | NA |
| Indica II | 465 | 56.60% | 0.00% | 2.15% | 41.29% | NA |
| Indica III | 913 | 2.10% | 0.00% | 5.48% | 92.44% | NA |
| Indica Intermediate | 786 | 15.40% | 0.00% | 3.69% | 80.92% | NA |
| Temperate Japonica | 767 | 94.30% | 2.20% | 1.04% | 2.48% | NA |
| Tropical Japonica | 504 | 84.70% | 0.00% | 1.19% | 14.09% | NA |
| Japonica Intermediate | 241 | 95.90% | 1.20% | 1.24% | 1.66% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 0.00% | 10.42% | NA |
| Intermediate | 90 | 66.70% | 1.10% | 2.22% | 30.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0700388228 | G -> DEL | LOC_Os07g01640.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0700388228 | G -> A | LOC_Os07g01640.1 | missense_variant ; p.Arg90His; MODERATE | nonsynonymous_codon ; R90H | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.677 |
DELETERIOUS | 0.03 |