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Detailed information for vg1117777877:
| Variant ID: vg1117777877 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17777877 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 128. )
Flanking Sequence (100 bp) in Reference Genome:
CTGGCGAAGAACAAGGGCACGTGGAGATCATGAGAGATTTGTCCCAGATTCGGAGAAAGAGATGCTGTGGACCACAATGCTCGAGACATTCACCCTTCCT[G/A]
CGGGTACAGAGGACAAAGTGAAAAGGTGGACTCTGAAGAAAATGGCAGAACAGTTTCAGAGCTTCAAGGGAGATCTGTACCAGAAGTATATACTGAAGGG
Reverse complement sequence
CCCTTCAGTATATACTTCTGGTACAGATCTCCCTTGAAGCTCTGAAACTGTTCTGCCATTTTCTTCAGAGTCCACCTTTTCACTTTGTCCTCTGTACCCG[C/T]
AGGAAGGGTGAATGTCTCGAGCATTGTGGTCCACAGCATCTCTTTCTCCGAATCTGGGACAAATCTCTCATGATCTCCACGTGCCCTTGTTCTTCGCCAG
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 | 0.30% | 0.10% | 3.45% | 96.13% | NA |
| All Indica | 2759 | 0.60% | 0.00% | 4.35% | 95.07% | NA |
| All Japonica | 1512 | 0.00% | 0.30% | 1.19% | 98.54% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.74% | 99.26% | NA |
| Indica I | 595 | 0.30% | 0.00% | 1.68% | 97.98% | NA |
| Indica II | 465 | 0.60% | 0.00% | 11.61% | 87.74% | NA |
| Indica III | 913 | 0.70% | 0.00% | 2.74% | 96.60% | NA |
| Indica Intermediate | 786 | 0.60% | 0.00% | 3.94% | 95.42% | NA |
| Temperate Japonica | 767 | 0.00% | 0.40% | 1.96% | 97.65% | NA |
| Tropical Japonica | 504 | 0.00% | 0.20% | 0.40% | 99.40% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 0.41% | 99.59% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 16.67% | 83.33% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 7.78% | 92.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117777877 | G -> A | LOC_Os11g30552.1 | missense_variant ; p.Ala277Thr; MODERATE | nonsynonymous_codon ; A277T | Average:11.062; most accessible tissue: Minghui63 panicle, score: 16.27 | benign  |
0.715 |
DELETERIOUS | 0.04 |
| vg1117777877 | G -> DEL | LOC_Os11g30552.1 | N | frameshift_variant | Average:11.062; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |