Search for Variation information by Variation ID:
Detailed information for vg0108238964:
| Variant ID: vg0108238964 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 8238964 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGGTGCTTCCGCCTGCACGGCAGACTTATTATGCTGCCGTTGTTGGGCGTCTACGTCTTCACCGACCGGCTCGCCTTCGTCGCCGCCGACTGGTGTCCAC[G/T]
CCTGCACGGCTGGCCTATTATGCCGCCGCTGTTGGGCGCCTACGTCTTCACCGACCGGCTCGCCTTCGCCGCCGCCGACTGGTGTCCTCGCCTGCACGGC
Reverse complement sequence
GCCGTGCAGGCGAGGACACCAGTCGGCGGCGGCGAAGGCGAGCCGGTCGGTGAAGACGTAGGCGCCCAACAGCGGCGGCATAATAGGCCAGCCGTGCAGG[C/A]
GTGGACACCAGTCGGCGGCGACGAAGGCGAGCCGGTCGGTGAAGACGTAGACGCCCAACAACGGCAGCATAATAAGTCTGCCGTGCAGGCGGAAGCACCA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.50% | 0.20% | 1.48% | 0.89% | NA |
| All Indica | 2759 | 97.50% | 0.30% | 0.98% | 1.27% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.13% | 0.20% | NA |
| Aus | 269 | 84.80% | 0.00% | 15.24% | 0.00% | NA |
| Indica I | 595 | 97.50% | 0.00% | 2.02% | 0.50% | NA |
| Indica II | 465 | 93.30% | 0.00% | 1.29% | 5.38% | NA |
| Indica III | 913 | 99.00% | 0.90% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 98.10% | 0.00% | 1.02% | 0.89% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 0.00% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0108238964 | G -> T | LOC_Os01g14730.1 | missense_variant ; p.Arg54Leu; MODERATE | nonsynonymous_codon ; R54L | Average:46.546; most accessible tissue: Minghui63 root, score: 63.193 | possibly damaging  |
1.589 |
DELETERIOUS | 0.01 |
| vg0108238964 | G -> DEL | LOC_Os01g14730.1 | N | frameshift_variant | Average:46.546; most accessible tissue: Minghui63 root, score: 63.193 | N | N | N | N |