Search for Variation information by Variation ID:
Detailed information for vg0435226127:
| Variant ID: vg0435226127 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 35226127 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGTAGGGGGCTCTGCGAGTGATCTTCTGAGCTCTCGCACTCTTTCGTGTGCGCCAAGCTTTTCCTGTTCAGCCCAATGGCCGAACAAGCAAAGGCGCACA[A/G]
CCTCTCTCCGAGTGTTAGCGGTGACGACGGGGAGCCAAACCCACGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAAAGTCCTAGGCGGGAGGAG
Reverse complement sequence
CTCCTCCCGCCTAGGACTTTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCGTGGGTTTGGCTCCCCGTCGTCACCGCTAACACTCGGAGAGAGG[T/C]
TGTGCGCCTTTGCTTGTTCGGCCATTGGGCTGAACAGGAAAAGCTTGGCGCACACGAAAGAGTGCGAGAGCTCAGAAGATCACTCGCAGAGCCCCCTACC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 70.10% | 0.10% | 10.11% | 19.74% | NA |
| All Indica | 2759 | 51.20% | 0.00% | 16.35% | 32.48% | NA |
| All Japonica | 1512 | 98.20% | 0.20% | 1.32% | 0.26% | NA |
| Aus | 269 | 91.80% | 0.00% | 0.74% | 7.43% | NA |
| Indica I | 595 | 32.10% | 0.00% | 24.71% | 43.19% | NA |
| Indica II | 465 | 40.90% | 0.00% | 21.94% | 37.20% | NA |
| Indica III | 913 | 65.10% | 0.00% | 8.76% | 26.18% | NA |
| Indica Intermediate | 786 | 55.60% | 0.00% | 15.52% | 28.88% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 97.00% | 0.00% | 2.38% | 0.60% | NA |
| Japonica Intermediate | 241 | 95.40% | 1.20% | 2.90% | 0.41% | NA |
| VI/Aromatic | 96 | 93.80% | 0.00% | 1.04% | 5.21% | NA |
| Intermediate | 90 | 86.70% | 0.00% | 4.44% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0435226127 | A -> DEL | LOC_Os04g59220.1 | N | frameshift_variant | Average:7.402; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |
| vg0435226127 | A -> G | LOC_Os04g59220.1 | missense_variant ; p.Asn9Ser; MODERATE | nonsynonymous_codon | Average:7.402; most accessible tissue: Zhenshan97 root, score: 10.511 | benign  |
0.273 |
TOLERATED | 0.15 |