Search for Variation information by Variation ID:
Detailed information for vg0131447795:
| Variant ID: vg0131447795 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31447795 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCACATCCGAAGCTTGCCGTTCGCCTTGGGAACGACCACCGGGTTCGCCAGCCACTCCGGATGGATGACCTCACGGATGAATCCGGCTTCCAGAAGTCGC[G/A]
CCACCTCCTCGCGGATGAAGGCTTGACGTTCCGGGGCCTGCCGCCGCACTTTCTGCCGGACCGGCCTTGCGCCCGGCCGCACGGCGAGACGGTGCTCAAT
Reverse complement sequence
ATTGAGCACCGTCTCGCCGTGCGGCCGGGCGCAAGGCCGGTCCGGCAGAAAGTGCGGCGGCAGGCCCCGGAACGTCAAGCCTTCATCCGCGAGGAGGTGG[C/T]
GCGACTTCTGGAAGCCGGATTCATCCGTGAGGTCATCCATCCGGAGTGGCTGGCGAACCCGGTGGTCGTTCCCAAGGCGAACGGCAAGCTTCGGATGTGC
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 | 44.50% | 0.40% | 14.18% | 40.92% | NA |
| All Indica | 2759 | 27.90% | 0.60% | 18.41% | 53.10% | NA |
| All Japonica | 1512 | 76.10% | 0.00% | 8.00% | 15.94% | NA |
| Aus | 269 | 12.30% | 0.00% | 11.15% | 76.58% | NA |
| Indica I | 595 | 20.50% | 1.30% | 12.44% | 65.71% | NA |
| Indica II | 465 | 19.40% | 0.60% | 13.12% | 66.88% | NA |
| Indica III | 913 | 38.80% | 0.00% | 23.99% | 37.24% | NA |
| Indica Intermediate | 786 | 25.80% | 0.80% | 19.59% | 53.82% | NA |
| Temperate Japonica | 767 | 72.80% | 0.00% | 13.95% | 13.30% | NA |
| Tropical Japonica | 504 | 90.50% | 0.00% | 0.79% | 8.73% | NA |
| Japonica Intermediate | 241 | 56.40% | 0.00% | 4.15% | 39.42% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 1.04% | 2.08% | NA |
| Intermediate | 90 | 66.70% | 0.00% | 11.11% | 22.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131447795 | G -> A | LOC_Os01g54660.1 | missense_variant ; p.Ala847Val; MODERATE | nonsynonymous_codon ; A847V | Average:21.937; most accessible tissue: Zhenshan97 panicle, score: 52.263 | benign  |
0.563 |
DELETERIOUS | 0.00 |
| vg0131447795 | G -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:21.937; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |