Search for Variation information by Variation ID:
Detailed information for vg0800164252:
| Variant ID: vg0800164252 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 164252 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCGGGTTAGGGGGCAACAGGCGGCCTGACACACGCCTCGCCCCGTCCCGTCGGAATGATGAGAGCCTCCAGGCACTCGTCCCTAGCCGGAGCCGGCGTGG[G/T]
AACTCCTAGAGTTGGCACGTCAGCCCCGGCCAGATACATTCCAGGCTTCATCGTAACCATTGCAAGGAAGTCATTGTATGAAGAAGGGCAGACGTGTAGC
Reverse complement sequence
GCTACACGTCTGCCCTTCTTCATACAATGACTTCCTTGCAATGGTTACGATGAAGCCTGGAATGTATCTGGCCGGGGCTGACGTGCCAACTCTAGGAGTT[C/A]
CCACGCCGGCTCCGGCTAGGGACGAGTGCCTGGAGGCTCTCATCATTCCGACGGGACGGGGCGAGGCGTGTGTCAGGCCGCCTGTTGCCCCCTAACCCGC
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 | 32.30% | 0.30% | 3.62% | 63.84% | NA |
| All Indica | 2759 | 5.30% | 0.40% | 2.21% | 92.06% | NA |
| All Japonica | 1512 | 87.40% | 0.00% | 0.07% | 12.57% | NA |
| Aus | 269 | 2.60% | 0.00% | 37.55% | 59.85% | NA |
| Indica I | 595 | 11.30% | 0.80% | 2.52% | 85.38% | NA |
| Indica II | 465 | 3.00% | 0.00% | 2.37% | 94.62% | NA |
| Indica III | 913 | 1.60% | 0.20% | 1.97% | 96.17% | NA |
| Indica Intermediate | 786 | 6.40% | 0.60% | 2.16% | 90.84% | NA |
| Temperate Japonica | 767 | 97.50% | 0.00% | 0.00% | 2.48% | NA |
| Tropical Japonica | 504 | 71.40% | 0.00% | 0.20% | 28.37% | NA |
| Japonica Intermediate | 241 | 88.40% | 0.00% | 0.00% | 11.62% | NA |
| VI/Aromatic | 96 | 14.60% | 0.00% | 3.12% | 82.29% | NA |
| Intermediate | 90 | 42.20% | 0.00% | 5.56% | 52.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0800164252 | G -> T | LOC_Os08g01250.1 | missense_variant ; p.Pro78Thr; MODERATE | nonsynonymous_codon ; P78T | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
1.196 |
TOLERATED | 0.34 |
| vg0800164252 | G -> DEL | LOC_Os08g01250.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |