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Detailed information for vg1126903458:
| Variant ID: vg1126903458 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26903458 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 31. )
Flanking Sequence (100 bp) in Reference Genome:
ATGTGGCTGATAACGGGGAAGAGGAGGAGGTAGGAGTCGATCCTGCTCTGAACATCCCTGAACTTTTCAGCCTGCCTCCCGGCCATCACCAACCTGTACA[T/C]
GGCGCTATTGTCCTGGCATGCCATCACAAGCTCGTGCGCCTCCCGGAGCGTGTCGTCGAGCCCGGTGAAGACGCGGCGGGCGAGCTGCTCGCACTCCTTC
Reverse complement sequence
GAAGGAGTGCGAGCAGCTCGCCCGCCGCGTCTTCACCGGGCTCGACGACACGCTCCGGGAGGCGCACGAGCTTGTGATGGCATGCCAGGACAATAGCGCC[A/G]
TGTACAGGTTGGTGATGGCCGGGAGGCAGGCTGAAAAGTTCAGGGATGTTCAGAGCAGGATCGACTCCTACCTCCTCCTCTTCCCCGTTATCAGCCACAT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 17.60% | 0.40% | 0.23% | 81.85% | NA |
| All Indica | 2759 | 8.50% | 0.60% | 0.25% | 90.69% | NA |
| All Japonica | 1512 | 37.70% | 0.10% | 0.13% | 62.10% | NA |
| Aus | 269 | 4.80% | 0.00% | 0.00% | 95.17% | NA |
| Indica I | 595 | 13.80% | 2.20% | 0.67% | 83.36% | NA |
| Indica II | 465 | 3.90% | 0.00% | 0.00% | 96.13% | NA |
| Indica III | 913 | 2.80% | 0.10% | 0.00% | 97.04% | NA |
| Indica Intermediate | 786 | 13.70% | 0.30% | 0.38% | 85.62% | NA |
| Temperate Japonica | 767 | 64.90% | 0.10% | 0.26% | 34.68% | NA |
| Tropical Japonica | 504 | 3.40% | 0.00% | 0.00% | 96.63% | NA |
| Japonica Intermediate | 241 | 22.80% | 0.00% | 0.00% | 77.18% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 14.40% | 0.00% | 2.22% | 83.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126903458 | T -> DEL | LOC_Os11g44460.1 | N | frameshift_variant | Average:15.068; most accessible tissue: Callus, score: 62.316 | N | N | N | N |
| vg1126903458 | T -> C | LOC_Os11g44460.1 | missense_variant ; p.Met73Val; MODERATE | nonsynonymous_codon ; M73V | Average:15.068; most accessible tissue: Callus, score: 62.316 | benign  |
-0.595 |
TOLERATED | 1.00 |