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Detailed information for vg1126903465:
| Variant ID: vg1126903465 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26903465 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 31. )
Flanking Sequence (100 bp) in Reference Genome:
TGATAACGGGGAAGAGGAGGAGGTAGGAGTCGATCCTGCTCTGAACATCCCTGAACTTTTCAGCCTGCCTCCCGGCCATCACCAACCTGTACATGGCGCT[A/C]
TTGTCCTGGCATGCCATCACAAGCTCGTGCGCCTCCCGGAGCGTGTCGTCGAGCCCGGTGAAGACGCGGCGGGCGAGCTGCTCGCACTCCTTCTTGTTCT
Reverse complement sequence
AGAACAAGAAGGAGTGCGAGCAGCTCGCCCGCCGCGTCTTCACCGGGCTCGACGACACGCTCCGGGAGGCGCACGAGCTTGTGATGGCATGCCAGGACAA[T/G]
AGCGCCATGTACAGGTTGGTGATGGCCGGGAGGCAGGCTGAAAAGTTCAGGGATGTTCAGAGCAGGATCGACTCCTACCTCCTCCTCTTCCCCGTTATCA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 17.40% | 0.40% | 0.19% | 82.04% | NA |
| All Indica | 2759 | 8.40% | 0.60% | 0.25% | 90.79% | NA |
| All Japonica | 1512 | 37.40% | 0.10% | 0.07% | 62.50% | NA |
| Aus | 269 | 4.80% | 0.00% | 0.00% | 95.17% | NA |
| Indica I | 595 | 13.80% | 2.40% | 0.50% | 83.36% | NA |
| Indica II | 465 | 4.50% | 0.00% | 0.00% | 95.48% | NA |
| Indica III | 913 | 2.40% | 0.10% | 0.00% | 97.48% | NA |
| Indica Intermediate | 786 | 13.50% | 0.10% | 0.51% | 85.88% | NA |
| Temperate Japonica | 767 | 64.40% | 0.10% | 0.13% | 35.33% | NA |
| Tropical Japonica | 504 | 3.40% | 0.00% | 0.00% | 96.63% | NA |
| Japonica Intermediate | 241 | 22.40% | 0.00% | 0.00% | 77.59% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 0.00% | 98.96% | NA |
| Intermediate | 90 | 14.40% | 0.00% | 1.11% | 84.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126903465 | A -> DEL | LOC_Os11g44460.1 | N | frameshift_variant | Average:15.179; most accessible tissue: Callus, score: 62.316 | N | N | N | N |
| vg1126903465 | A -> C | LOC_Os11g44460.1 | missense_variant ; p.Asn70Lys; MODERATE | nonsynonymous_codon | Average:15.179; most accessible tissue: Callus, score: 62.316 | possibly damaging  |
-1.979 |
TOLERATED | 0.89 |