Search for Variation information by Variation ID:
Detailed information for vg0334135606:
| Variant ID: vg0334135606 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34135606 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGGAAAGAAGGGCAGAGGGCCTGATGAGCCTAAGCGTCAAGTGGTTCTCCCAGGCAAAAGAAAAATCGTCGGAGTTGAGGACAAGACTGACGAGGATTAC[G/A]
ATCAGTTGGATGGGCAACCCCCTTTCACGGTGACGATTGACCCTAGCATCCTCCTATCAAATGAAGACACCCCTTACTCACGCAGCGATCACAAGGAGGG
Reverse complement sequence
CCCTCCTTGTGATCGCTGCGTGAGTAAGGGGTGTCTTCATTTGATAGGAGGATGCTAGGGTCAATCGTCACCGTGAAAGGGGGTTGCCCATCCAACTGAT[C/T]
GTAATCCTCGTCAGTCTTGTCCTCAACTCCGACGATTTTTCTTTTGCCTGGGAGAACCACTTGACGCTTAGGCTCATCAGGCCCTCTGCCCTTCTTTCCT
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 | 43.80% | 1.00% | 8.80% | 46.45% | NA |
| All Indica | 2759 | 17.90% | 0.10% | 9.79% | 72.24% | NA |
| All Japonica | 1512 | 91.00% | 2.90% | 4.23% | 1.85% | NA |
| Aus | 269 | 21.20% | 0.00% | 30.11% | 48.70% | NA |
| Indica I | 595 | 13.90% | 0.00% | 1.34% | 84.71% | NA |
| Indica II | 465 | 5.80% | 0.40% | 7.53% | 86.24% | NA |
| Indica III | 913 | 28.10% | 0.00% | 16.76% | 55.09% | NA |
| Indica Intermediate | 786 | 16.20% | 0.00% | 9.41% | 74.43% | NA |
| Temperate Japonica | 767 | 89.40% | 3.90% | 6.39% | 0.26% | NA |
| Tropical Japonica | 504 | 92.50% | 0.60% | 2.18% | 4.76% | NA |
| Japonica Intermediate | 241 | 92.90% | 4.60% | 1.66% | 0.83% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 55.60% | 1.10% | 1.11% | 42.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334135606 | G -> A | LOC_Os03g60010.1 | missense_variant ; p.Asp1059Asn; MODERATE | nonsynonymous_codon ; D1059N | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.336 |
DELETERIOUS | 0.04 |
| vg0334135606 | G -> DEL | LOC_Os03g60010.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |