Search for Variation information by Variation ID:
Detailed information for vg0108457609:
| Variant ID: vg0108457609 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 8457609 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.81, G: 0.18, others allele: 0.00, population size: 159. )
Flanking Sequence (100 bp) in Reference Genome:
GCCGGATATCGACTTGAAGGATAGGCATGGCTATTCCCCTACGGTGTCTCCGGATACCGTCAGGAGATACGAAAGCGCTATCTCTGATCTCGCCGGGCAC[A/G]
GATTCGAGGAGGAAGACTACCCTGTTGTCGACTACGAGTCAGACCTTCAGACCGACATGTCCACAACAGTTAGATAGGCTACCCACATATTGTACTGGTG
Reverse complement sequence
CACCAGTACAATATGTGGGTAGCCTATCTAACTGTTGTGGACATGTCGGTCTGAAGGTCTGACTCGTAGTCGACAACAGGGTAGTCTTCCTCCTCGAATC[T/C]
GTGCCCGGCGAGATCAGAGATAGCGCTTTCGTATCTCCTGACGGTATCCGGAGACACCGTAGGGGAATAGCCATGCCTATCCTTCAAGTCGATATCCGGC
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 | 43.30% | 7.40% | 17.54% | 31.80% | NA |
| All Indica | 2759 | 34.10% | 3.90% | 18.74% | 43.28% | NA |
| All Japonica | 1512 | 64.10% | 0.20% | 17.26% | 18.45% | NA |
| Aus | 269 | 13.00% | 85.90% | 0.74% | 0.37% | NA |
| Indica I | 595 | 46.10% | 0.20% | 20.50% | 33.28% | NA |
| Indica II | 465 | 31.60% | 2.40% | 18.28% | 47.74% | NA |
| Indica III | 913 | 25.30% | 5.00% | 19.50% | 50.16% | NA |
| Indica Intermediate | 786 | 36.80% | 6.20% | 16.79% | 40.20% | NA |
| Temperate Japonica | 767 | 85.40% | 0.00% | 8.87% | 5.74% | NA |
| Tropical Japonica | 504 | 36.70% | 0.60% | 26.39% | 36.31% | NA |
| Japonica Intermediate | 241 | 53.50% | 0.00% | 24.90% | 21.58% | NA |
| VI/Aromatic | 96 | 58.30% | 3.10% | 23.96% | 14.58% | NA |
| Intermediate | 90 | 48.90% | 5.60% | 28.89% | 16.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0108457609 | A -> G | LOC_Os01g15070.1 | missense_variant ; p.Arg62Gly; MODERATE | nonsynonymous_codon ; R62G | Average:53.642; most accessible tissue: Zhenshan97 panicle, score: 68.538 | benign  |
-0.892 |
TOLERATED | 1.00 |
| vg0108457609 | A -> DEL | LOC_Os01g15070.1 | N | frameshift_variant | Average:53.642; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |