Search for Variation information by Variation ID:
Detailed information for vg0625222863:
| Variant ID: vg0625222863 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 25222863 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTATGCAAGATAAATGACATAATTGTTGGAAGTAATACAAATTGGACGTACCGCCACGAAGTAGTCTCGGTCACGGTGCGTGGGATACGCGTCCGTGACA[G/A]
CGGCAACGTGCGGCTCTGGGGCGTCTGGAGTGAAGGTCACACGCGCACGAGTGCGAGGAAGGTACCAGCGAAGGTCACACTTGCTGCAGCGTAAAGTCCT
Reverse complement sequence
AGGACTTTACGCTGCAGCAAGTGTGACCTTCGCTGGTACCTTCCTCGCACTCGTGCGCGTGTGACCTTCACTCCAGACGCCCCAGAGCCGCACGTTGCCG[C/T]
TGTCACGGACGCGTATCCCACGCACCGTGACCGAGACTACTTCGTGGCGGTACGTCCAATTTGTATTACTTCCAACAATTATGTCATTTATCTTGCATAA
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 | 15.60% | 0.20% | 5.01% | 79.24% | NA |
| All Indica | 2759 | 0.80% | 0.00% | 3.23% | 95.98% | NA |
| All Japonica | 1512 | 45.90% | 0.10% | 5.36% | 48.68% | NA |
| Aus | 269 | 2.20% | 0.00% | 13.38% | 84.39% | NA |
| Indica I | 595 | 0.70% | 0.00% | 0.67% | 98.66% | NA |
| Indica II | 465 | 1.10% | 0.00% | 2.58% | 96.34% | NA |
| Indica III | 913 | 0.30% | 0.00% | 4.27% | 95.40% | NA |
| Indica Intermediate | 786 | 1.30% | 0.00% | 4.33% | 94.40% | NA |
| Temperate Japonica | 767 | 72.60% | 0.00% | 0.78% | 26.60% | NA |
| Tropical Japonica | 504 | 8.10% | 0.20% | 11.31% | 80.36% | NA |
| Japonica Intermediate | 241 | 39.80% | 0.00% | 7.47% | 52.70% | NA |
| VI/Aromatic | 96 | 6.20% | 7.30% | 23.96% | 62.50% | NA |
| Intermediate | 90 | 8.90% | 0.00% | 8.89% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0625222863 | G -> A | LOC_Os06g42010.1 | missense_variant ; p.Ala762Val; MODERATE | nonsynonymous_codon ; A762V | Average:4.868; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.382 |
DELETERIOUS | 0.00 |
| vg0625222863 | G -> DEL | LOC_Os06g42010.1 | N | frameshift_variant | Average:4.868; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |