Search for Variation information by Variation ID:
Detailed information for vg0329363160:
| Variant ID: vg0329363160 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 29363160 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGCGCTTCGTCGGCGAGGGGGGTGTAGAACCAGTCGCTCTTCCAGTCATCCCACTTCTTGCGGAGGACGCAGGGAATGTAGCGGTTCAACACCGGCCCCC[G/A]
CGGCTGGAAGTAGCAACCACCAACCACCGACGGCGGCGACACCGACTGTACGGTGAAGAACCACCGGAACAGCCGAAGGGATGGGCGCACCCCGATGAAC
Reverse complement sequence
GTTCATCGGGGTGCGCCCATCCCTTCGGCTGTTCCGGTGGTTCTTCACCGTACAGTCGGTGTCGCCGCCGTCGGTGGTTGGTGGTTGCTACTTCCAGCCG[C/T]
GGGGGCCGGTGTTGAACCGCTACATTCCCTGCGTCCTCCGCAAGAAGTGGGATGACTGGAAGAGCGACTGGTTCTACACCCCCCTCGCCGACGAAGCGCG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.80% | 0.40% | 1.71% | 41.09% | NA |
| All Indica | 2759 | 37.80% | 0.70% | 2.46% | 59.12% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.07% | 0.40% | NA |
| Aus | 269 | 1.90% | 0.00% | 1.49% | 96.65% | NA |
| Indica I | 595 | 53.30% | 0.00% | 1.34% | 45.38% | NA |
| Indica II | 465 | 38.50% | 0.00% | 1.51% | 60.00% | NA |
| Indica III | 913 | 28.10% | 1.20% | 2.96% | 67.69% | NA |
| Indica Intermediate | 786 | 36.80% | 0.90% | 3.31% | 59.03% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 75.00% | 0.00% | 7.29% | 17.71% | NA |
| Intermediate | 90 | 66.70% | 1.10% | 1.11% | 31.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0329363160 | G -> A | LOC_Os03g51320.1 | missense_variant ; p.Arg140Trp; MODERATE | nonsynonymous_codon ; R140W | Average:25.615; most accessible tissue: Zhenshan97 flag leaf, score: 58.772 | benign  |
0.88 |
DELETERIOUS | 0.02 |
| vg0329363160 | G -> DEL | LOC_Os03g51320.1 | N | frameshift_variant | Average:25.615; most accessible tissue: Zhenshan97 flag leaf, score: 58.772 | N | N | N | N |