Search for Variation information by Variation ID:
Detailed information for vg0329361688:
| Variant ID: vg0329361688 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 29361688 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TGCTTGCAGGGCCTCCACCTGGGCACTTAACCCGTCCAACACCGTGGTGTTTGCGATGGCCAAGGCCTGCAGAAGGGGTTCTGCGCTCAGTGGAGCAACG[G/A]
AAGGCGTGGGGAAGAGCCGCCTCGAAGAGGATGCTGCGCGGCTTGGCCCGCCGATGGACGTGCCGGACTCGGGGATGTCCCCCGGACCTGGTTTGTCCTG
Reverse complement sequence
CAGGACAAACCAGGTCCGGGGGACATCCCCGAGTCCGGCACGTCCATCGGCGGGCCAAGCCGCGCAGCATCCTCTTCGAGGCGGCTCTTCCCCACGCCTT[C/T]
CGTTGCTCCACTGAGCGCAGAACCCCTTCTGCAGGCCTTGGCCATCGCAAACACCACGGTGTTGGACGGGTTAAGTGCCCAGGTGGAGGCCCTGCAAGCA
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 | 69.40% | 0.90% | 13.50% | 16.17% | NA |
| All Indica | 2759 | 61.40% | 0.00% | 21.71% | 16.93% | NA |
| All Japonica | 1512 | 97.30% | 2.30% | 0.40% | 0.00% | NA |
| Aus | 269 | 2.60% | 0.00% | 1.49% | 95.91% | NA |
| Indica I | 595 | 60.20% | 0.00% | 25.04% | 14.79% | NA |
| Indica II | 465 | 57.80% | 0.00% | 23.66% | 18.49% | NA |
| Indica III | 913 | 65.80% | 0.00% | 15.44% | 18.73% | NA |
| Indica Intermediate | 786 | 59.20% | 0.00% | 25.32% | 15.52% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 94.20% | 5.20% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.40% | 3.70% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 45.80% | 8.30% | 22.92% | 22.92% | NA |
| Intermediate | 90 | 72.20% | 1.10% | 7.78% | 18.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0329361688 | G -> A | LOC_Os03g51320.1 | missense_variant ; p.Ser559Phe; MODERATE | nonsynonymous_codon ; S559F | Average:34.951; most accessible tissue: Zhenshan97 flower, score: 75.194 | benign  |
0.815 |
DELETERIOUS | 0.01 |
| vg0329361688 | G -> DEL | LOC_Os03g51320.1 | N | frameshift_variant | Average:34.951; most accessible tissue: Zhenshan97 flower, score: 75.194 | N | N | N | N |