Search for Variation information by Variation ID:
Detailed information for vg0137499643:
| Variant ID: vg0137499643 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 37499643 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGGTGAGAGACGAACCTGCGAGGGGGTCGGTTAAACGACCACTTTGGAGGGGAAATAAGGTTTCCCCGAGATGGTTCTGTCTCCCCCATCTTACGGGGCC[A/G]
CTTCTTCTTGCGCTCCCCCTCGGGCTGCGATGTTGGCGCGGCCCCCTCCGGGCGCCTGTTACTGGCACGCGCCGCCCCGCCCCCTCGGGGAGGAGATGGG
Reverse complement sequence
CCCATCTCCTCCCCGAGGGGGCGGGGCGGCGCGTGCCAGTAACAGGCGCCCGGAGGGGGCCGCGCCAACATCGCAGCCCGAGGGGGAGCGCAAGAAGAAG[T/C]
GGCCCCGTAAGATGGGGGAGACAGAACCATCTCGGGGAAACCTTATTTCCCCTCCAAAGTGGTCGTTTAACCGACCCCCTCGCAGGTTCGTCTCTCACCC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.90% | 0.20% | 8.27% | 90.63% | NA |
| All Indica | 2759 | 0.00% | 0.10% | 0.94% | 98.99% | NA |
| All Japonica | 1512 | 2.70% | 0.50% | 19.58% | 77.18% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.37% | 99.63% | NA |
| Indica I | 595 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Indica II | 465 | 0.00% | 0.20% | 0.43% | 99.35% | NA |
| Indica III | 913 | 0.00% | 0.00% | 0.44% | 99.56% | NA |
| Indica Intermediate | 786 | 0.00% | 0.10% | 2.54% | 97.33% | NA |
| Temperate Japonica | 767 | 4.40% | 0.10% | 13.04% | 82.40% | NA |
| Tropical Japonica | 504 | 0.60% | 1.20% | 32.34% | 65.87% | NA |
| Japonica Intermediate | 241 | 1.70% | 0.40% | 13.69% | 84.23% | NA |
| VI/Aromatic | 96 | 0.00% | 1.00% | 43.75% | 55.21% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 28.89% | 71.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0137499643 | A -> G | LOC_Os01g64610.1 | missense_variant ; p.Trp359Arg; MODERATE | nonsynonymous_codon ; W359R | Average:5.952; most accessible tissue: Callus, score: 12.634 | benign  |
-0.338 |
TOLERATED | 1.00 |
| vg0137499643 | A -> DEL | LOC_Os01g64610.1 | N | frameshift_variant | Average:5.952; most accessible tissue: Callus, score: 12.634 | N | N | N | N |