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Detailed information for vg1126903423:
| Variant ID: vg1126903423 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26903423 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 35. )
Flanking Sequence (100 bp) in Reference Genome:
TATTCTCTTAATAGGCTGGACGACGAGTGATGTCCATGTGGCTGATAACGGGGAAGAGGAGGAGGTAGGAGTCGATCCTGCTCTGAACATCCCTGAACTT[T/G]
TCAGCCTGCCTCCCGGCCATCACCAACCTGTACATGGCGCTATTGTCCTGGCATGCCATCACAAGCTCGTGCGCCTCCCGGAGCGTGTCGTCGAGCCCGG
Reverse complement sequence
CCGGGCTCGACGACACGCTCCGGGAGGCGCACGAGCTTGTGATGGCATGCCAGGACAATAGCGCCATGTACAGGTTGGTGATGGCCGGGAGGCAGGCTGA[A/C]
AAGTTCAGGGATGTTCAGAGCAGGATCGACTCCTACCTCCTCCTCTTCCCCGTTATCAGCCACATGGACATCACTCGTCGTCCAGCCTATTAAGAGAATA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 46.70% | 18.40% | 3.75% | 31.17% | NA |
| All Indica | 2759 | 47.20% | 9.70% | 3.12% | 39.98% | NA |
| All Japonica | 1512 | 41.30% | 36.40% | 3.90% | 18.32% | NA |
| Aus | 269 | 60.20% | 12.30% | 8.18% | 19.33% | NA |
| Indica I | 595 | 33.10% | 16.30% | 3.03% | 47.56% | NA |
| Indica II | 465 | 61.50% | 4.50% | 0.65% | 33.33% | NA |
| Indica III | 913 | 50.30% | 3.20% | 4.49% | 42.06% | NA |
| Indica Intermediate | 786 | 45.70% | 15.50% | 3.05% | 35.75% | NA |
| Temperate Japonica | 767 | 19.80% | 63.40% | 2.35% | 14.47% | NA |
| Tropical Japonica | 504 | 68.80% | 3.20% | 6.55% | 21.43% | NA |
| Japonica Intermediate | 241 | 52.30% | 20.30% | 3.32% | 24.07% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 3.12% | 12.50% | NA |
| Intermediate | 90 | 43.30% | 16.70% | 7.78% | 32.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126903423 | T -> DEL | LOC_Os11g44460.1 | N | frameshift_variant | Average:14.505; most accessible tissue: Callus, score: 46.436 | N | N | N | N |
| vg1126903423 | T -> G | LOC_Os11g44460.1 | missense_variant ; p.Glu84Asp; MODERATE | nonsynonymous_codon ; E84D | Average:14.505; most accessible tissue: Callus, score: 46.436 | benign  |
0.317 |
TOLERATED | 1.00 |