Search for Variation information by Variation ID:
Detailed information for vg0322194116:
| Variant ID: vg0322194116 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22194116 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCCTGGTAGCTTGCCAGTACGAGCTCCACCGCCCCCCGGGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAGCTCCTCGGGGAGCCGCTGGAGGG[C/T]
CCCGGCCATCTCTGAGAGGCACTGGGCGAGGCCCCCCTGGTTGGCGGCGTACTTCGCGTGCCGCCCGCCCCAGAGACCCGCCTGCCGCCCGGCGCGGTCT
Reverse complement sequence
AGACCGCGCCGGGCGGCAGGCGGGTCTCTGGGGCGGGCGGCACGCGAAGTACGCCGCCAACCAGGGGGGCCTCGCCCAGTGCCTCTCAGAGATGGCCGGG[G/A]
CCCTCCAGCGGCTCCCCGAGGAGCTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCCCGGGGGGCGGTGGAGCTCGTACTGGCAAGCTACCAGGC
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 | 10.10% | 0.80% | 11.70% | 77.42% | NA |
| All Indica | 2759 | 3.30% | 1.20% | 15.40% | 80.03% | NA |
| All Japonica | 1512 | 24.80% | 0.00% | 5.82% | 69.38% | NA |
| Aus | 269 | 0.40% | 1.10% | 10.78% | 87.73% | NA |
| Indica I | 595 | 0.20% | 0.80% | 3.87% | 95.13% | NA |
| Indica II | 465 | 1.10% | 0.20% | 3.66% | 95.05% | NA |
| Indica III | 913 | 7.30% | 2.30% | 32.09% | 58.27% | NA |
| Indica Intermediate | 786 | 2.40% | 0.90% | 11.70% | 84.99% | NA |
| Temperate Japonica | 767 | 11.00% | 0.00% | 3.39% | 85.66% | NA |
| Tropical Japonica | 504 | 47.40% | 0.00% | 10.32% | 42.26% | NA |
| Japonica Intermediate | 241 | 21.60% | 0.00% | 4.15% | 74.27% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 1.04% | 97.92% | NA |
| Intermediate | 90 | 8.90% | 0.00% | 11.11% | 80.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322194116 | C -> T | LOC_Os03g39930.1 | missense_variant ; p.Ala336Thr; MODERATE | nonsynonymous_codon ; A336T | Average:6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 | benign  |
0.105 |
TOLERATED | 0.91 |
| vg0322194116 | C -> DEL | LOC_Os03g39930.1 | N | frameshift_variant | Average:6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |