Search for Variation information by Variation ID:
Detailed information for vg0329363433:
| Variant ID: vg0329363433 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 29363433 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TAAAACTCCAGAACATCCATGAAGAAAGAAGAAAATGGCGGAACCAGCCCTGCCATTGCAAAAGGGAGGAAGAAGACGGACCGCCCCGGGTAGCATGGCG[T/C]
CGGGCGTCCCTCGCCCAGCGTAACTATCTCCCGGCCGGTGGCAGATTCCGGCATGAAGCGGCGTGGCAGCCCGGCCTGCCTCTCGCTCACGATGCGGGAA
Reverse complement sequence
TTCCCGCATCGTGAGCGAGAGGCAGGCCGGGCTGCCACGCCGCTTCATGCCGGAATCTGCCACCGGCCGGGAGATAGTTACGCTGGGCGAGGGACGCCCG[A/G]
CGCCATGCTACCCGGGGCGGTCCGTCTTCTTCCTCCCTTTTGCAATGGCAGGGCTGGTTCCGCCATTTTCTTCTTTCTTCATGGATGTTCTGGAGTTTTA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.70% | 0.40% | 0.66% | 42.19% | NA |
| All Indica | 2759 | 38.50% | 0.00% | 0.91% | 60.57% | NA |
| All Japonica | 1512 | 99.50% | 0.10% | 0.00% | 0.46% | NA |
| Aus | 269 | 2.20% | 0.00% | 1.86% | 95.91% | NA |
| Indica I | 595 | 53.30% | 0.00% | 0.67% | 46.05% | NA |
| Indica II | 465 | 39.60% | 0.00% | 2.37% | 58.06% | NA |
| Indica III | 913 | 28.70% | 0.00% | 0.55% | 70.76% | NA |
| Indica Intermediate | 786 | 38.20% | 0.00% | 0.64% | 61.20% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 52.10% | 18.80% | 1.04% | 28.12% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 0.00% | 34.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0329363433 | T -> C | LOC_Os03g51320.1 | missense_variant ; p.Thr49Ala; MODERATE | nonsynonymous_codon ; T49A | Average:25.675; most accessible tissue: Zhenshan97 flag leaf, score: 65.3 | benign  |
-0.586 |
TOLERATED | 1.00 |
| vg0329363433 | T -> DEL | LOC_Os03g51320.1 | N | frameshift_variant | Average:25.675; most accessible tissue: Zhenshan97 flag leaf, score: 65.3 | N | N | N | N |