Search for Variation information by Variation ID:
Detailed information for vg0321793551:
| Variant ID: vg0321793551 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 21793551 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTCACGCGTGGCGCCGCCGCCTTCGCGGGGGAGGAGGAGATCGTGCAGGCGCTGCAGAAGCACGCCGCGACGGCCGAGGCGGAGATTGCGGAATCACAAG[C/T]
GTTCTCTGCGGTCTTGTTAGCCGATGCCAACCGAGCAGCAAGTCCCGTCGTCGTCGTGCATAAGAGGCCGACACCGGAGACGGAGAAGGAGCAGGATCAG
Reverse complement sequence
CTGATCCTGCTCCTTCTCCGTCTCCGGTGTCGGCCTCTTATGCACGACGACGACGGGACTTGCTGCTCGGTTGGCATCGGCTAACAAGACCGCAGAGAAC[G/A]
CTTGTGATTCCGCAATCTCCGCCTCGGCCGTCGCGGCGTGCTTCTGCAGCGCCTGCACGATCTCCTCCTCCCCCGCGAAGGCGGCGGCGCCACGCGTGAG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.70% | 0.10% | 1.76% | 1.42% | NA |
| All Indica | 2759 | 97.30% | 0.00% | 1.81% | 0.87% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 70.60% | 1.90% | 12.27% | 15.24% | NA |
| Indica I | 595 | 98.30% | 0.00% | 1.68% | 0.00% | NA |
| Indica II | 465 | 98.70% | 0.00% | 0.86% | 0.43% | NA |
| Indica III | 913 | 96.70% | 0.00% | 1.64% | 1.64% | NA |
| Indica Intermediate | 786 | 96.40% | 0.00% | 2.67% | 0.89% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 0.00% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0321793551 | C -> T | LOC_Os03g39240.1 | missense_variant ; p.Ala231Val; MODERATE | nonsynonymous_codon ; A231V | Average:38.668; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 | benign  |
1.126 |
DELETERIOUS | 0.00 |
| vg0321793551 | C -> DEL | LOC_Os03g39240.1 | N | frameshift_variant | Average:38.668; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 | N | N | N | N |