Search for Variation information by Variation ID:
Detailed information for vg0233354790:
| Variant ID: vg0233354790 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 33354790 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AACAGGCGCGGGAGGGCCGAGAAGTAGTCGTACGTCTTGCCGTCGTTCATGTTCTCGGTGCAGTTGAGCACGAGGATGTCGCCGTGGGTGATGATCTCCA[T/G]
CGCCACCAGCACGGCGTCCTCCTCCTTGTCCAGGCTGCACATCACGAAGCGGACGTCGATGGCGGCGCGCCGCGGCGGCGGCTGGAGCGCGTACGCCATG
Reverse complement sequence
CATGGCGTACGCGCTCCAGCCGCCGCCGCGGCGCGCCGCCATCGACGTCCGCTTCGTGATGTGCAGCCTGGACAAGGAGGAGGACGCCGTGCTGGTGGCG[A/C]
TGGAGATCATCACCCACGGCGACATCCTCGTGCTCAACTGCACCGAGAACATGAACGACGGCAAGACGTACGACTACTTCTCGGCCCTCCCGCGCCTGTT
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 | 64.40% | 35.50% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 98.60% | 1.40% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 1.00% | 98.90% | 0.07% | 0.00% | NA |
| Aus | 269 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.20% | 0.17% | 0.00% | NA |
| Indica II | 465 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.30% | 2.50% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 1.20% | 98.70% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 0.00% | 100.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.50% | 97.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 10.40% | 89.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 42.20% | 55.60% | 2.22% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0233354790 | T -> G | LOC_Os02g54450.1 | missense_variant ; p.Met110Leu; MODERATE | nonsynonymous_codon ; M110L | Average:71.413; most accessible tissue: Zhenshan97 root, score: 80.68 | benign  |
-0.848 |
TOLERATED | 1.00 |