Search for Variation information by Variation ID:
Detailed information for vg0135356886:
| Variant ID: vg0135356886 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 35356886 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 107. )
Flanking Sequence (100 bp) in Reference Genome:
TGCAGTGATCTCCTCCTTCCACCCAAAAACACCGTCCACGGGACCAACTGGTGCTCCCGCCAGCGGTAGCCCGAGCAGGTACGACACGTCCTGCAGTGTC[G/A]
GAGCCATCTCCCCACAGGGAAGGTGGAACGTGTGCGTCTCAGGTCTCCAGCGGTCTACTAGAGCGGCAAGGAGTGACCGGTCTGCATCCCACCGCTTCGC
Reverse complement sequence
GCGAAGCGGTGGGATGCAGACCGGTCACTCCTTGCCGCTCTAGTAGACCGCTGGAGACCTGAGACGCACACGTTCCACCTTCCCTGTGGGGAGATGGCTC[C/T]
GACACTGCAGGACGTGTCGTACCTGCTCGGGCTACCGCTGGCGGGAGCACCAGTTGGTCCCGTGGACGGTGTTTTTGGGTGGAAGGAGGAGATCACTGCA
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 | 7.60% | 0.10% | 15.93% | 76.39% | NA |
| All Indica | 2759 | 1.10% | 0.20% | 0.62% | 98.12% | NA |
| All Japonica | 1512 | 19.40% | 0.00% | 43.45% | 37.17% | NA |
| Aus | 269 | 0.00% | 0.40% | 1.12% | 98.51% | NA |
| Indica I | 595 | 2.20% | 0.20% | 1.01% | 96.64% | NA |
| Indica II | 465 | 0.40% | 0.40% | 0.00% | 99.14% | NA |
| Indica III | 913 | 0.10% | 0.10% | 0.11% | 99.67% | NA |
| Indica Intermediate | 786 | 1.80% | 0.10% | 1.27% | 96.82% | NA |
| Temperate Japonica | 767 | 12.30% | 0.00% | 40.68% | 47.07% | NA |
| Tropical Japonica | 504 | 28.80% | 0.00% | 46.03% | 25.20% | NA |
| Japonica Intermediate | 241 | 22.40% | 0.00% | 46.89% | 30.71% | NA |
| VI/Aromatic | 96 | 26.00% | 0.00% | 47.92% | 26.04% | NA |
| Intermediate | 90 | 10.00% | 0.00% | 33.33% | 56.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0135356886 | G -> A | LOC_Os01g61090.1 | missense_variant ; p.Pro983Leu; MODERATE | nonsynonymous_codon ; P983L | Average:33.792; most accessible tissue: Zhenshan97 flag leaf, score: 75.143 | benign  |
0.274 |
DELETERIOUS | 0.02 |
| vg0135356886 | G -> DEL | LOC_Os01g61090.1 | N | frameshift_variant | Average:33.792; most accessible tissue: Zhenshan97 flag leaf, score: 75.143 | N | N | N | N |