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Detailed information for vg1117779730:
| Variant ID: vg1117779730 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17779730 |
| 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: 318. )
Flanking Sequence (100 bp) in Reference Genome:
GCCGTTGGTGACCGGTAAAGAAATGACGATAGAACAATTTATTACTGACACTGGTCTAACTACGGATCAATTGCTAGGAGTCGCACCAATCGAAAAGGCG[G/A]
AAGTGAAATACATGTACGAACTCGGTAAACCGCTTGTCAAGCCTGAGCTGCTGCAGTCCCTACCCACACAAATGTACAAGTTCCATCAGCTGTACATGGA
Reverse complement sequence
TCCATGTACAGCTGATGGAACTTGTACATTTGTGTGGGTAGGGACTGCAGCAGCTCAGGCTTGACAAGCGGTTTACCGAGTTCGTACATGTATTTCACTT[C/T]
CGCCTTTTCGATTGGTGCGACTCCTAGCAATTGATCCGTAGTTAGACCAGTGTCAGTAATAAATTGTTCTATCGTCATTTCTTTACCGGTCACCAACGGC
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 | 25.00% | 0.10% | 1.69% | 73.17% | NA |
| All Indica | 2759 | 8.70% | 0.20% | 1.56% | 89.56% | NA |
| All Japonica | 1512 | 53.00% | 0.00% | 2.05% | 44.97% | NA |
| Aus | 269 | 8.90% | 0.00% | 1.49% | 89.59% | NA |
| Indica I | 595 | 6.40% | 0.00% | 1.18% | 92.44% | NA |
| Indica II | 465 | 24.10% | 0.00% | 1.29% | 74.62% | NA |
| Indica III | 913 | 3.20% | 0.50% | 1.75% | 94.52% | NA |
| Indica Intermediate | 786 | 7.80% | 0.00% | 1.78% | 90.46% | NA |
| Temperate Japonica | 767 | 60.80% | 0.00% | 4.04% | 35.20% | NA |
| Tropical Japonica | 504 | 27.60% | 0.00% | 0.00% | 72.42% | NA |
| Japonica Intermediate | 241 | 81.30% | 0.00% | 0.00% | 18.67% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 33.30% | 0.00% | 2.22% | 64.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117779730 | G -> A | LOC_Os11g30552.1 | missense_variant ; p.Glu870Lys; MODERATE | nonsynonymous_codon ; E870K | Average:4.602; most accessible tissue: Zhenshan97 flag leaf, score: 7.948 | benign  |
0.638 |
DELETERIOUS | 0.02 |
| vg1117779730 | G -> DEL | LOC_Os11g30552.1 | N | frameshift_variant | Average:4.602; most accessible tissue: Zhenshan97 flag leaf, score: 7.948 | N | N | N | N |