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Detailed information for vg0512019766:
| Variant ID: vg0512019766 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12019766 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.01, others allele: 0.00, population size: 105. )
Flanking Sequence (100 bp) in Reference Genome:
AAAATTCCATTTAAACAACAATTTATAAATTTTAAAATTTTCAGGGTGTGACAAACCTACCCCCCTTAAACAGAATCTCGTCCTCGAGATTCGGAAGAAC[T/A]
GGCGAACAGGTGCGGATGAGCTGACTTCAATTCATCTTCTCGTTCCCAAGTTGATTCTTCTTCCGAGTGATTACTCCATTGAACTTTGCAGAAACGGATA
Reverse complement sequence
TATCCGTTTCTGCAAAGTTCAATGGAGTAATCACTCGGAAGAAGAATCAACTTGGGAACGAGAAGATGAATTGAAGTCAGCTCATCCGCACCTGTTCGCC[A/T]
GTTCTTCCGAATCTCGAGGACGAGATTCTGTTTAAGGGGGGTAGGTTTGTCACACCCTGAAAATTTTAAAATTTATAAATTGTTGTTTAAATGGAATTTT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 9.40% | 0.50% | 79.83% | 10.24% | NA |
| All Indica | 2759 | 7.40% | 0.80% | 84.85% | 7.00% | NA |
| All Japonica | 1512 | 14.30% | 0.00% | 80.75% | 4.96% | NA |
| Aus | 269 | 2.60% | 0.40% | 20.45% | 76.58% | NA |
| Indica I | 595 | 5.40% | 0.50% | 90.42% | 3.70% | NA |
| Indica II | 465 | 6.70% | 0.20% | 89.89% | 3.23% | NA |
| Indica III | 913 | 9.40% | 1.20% | 80.94% | 8.43% | NA |
| Indica Intermediate | 786 | 6.90% | 0.90% | 82.19% | 10.05% | NA |
| Temperate Japonica | 767 | 16.80% | 0.00% | 75.49% | 7.69% | NA |
| Tropical Japonica | 504 | 9.30% | 0.00% | 89.09% | 1.59% | NA |
| Japonica Intermediate | 241 | 16.60% | 0.00% | 80.08% | 3.32% | NA |
| VI/Aromatic | 96 | 12.50% | 0.00% | 86.46% | 1.04% | NA |
| Intermediate | 90 | 7.80% | 1.10% | 81.11% | 10.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512019766 | T -> DEL | LOC_Os05g20480.1 | N | frameshift_variant | Average:13.455; most accessible tissue: Minghui63 young leaf, score: 22.423 | N | N | N | N |
| vg0512019766 | T -> A | LOC_Os05g20480.1 | missense_variant ; p.Ser1233Cys; MODERATE | nonsynonymous_codon ; S1233C | Average:13.455; most accessible tissue: Minghui63 young leaf, score: 22.423 | probably damaging  |
3.215 |
DELETERIOUS | 0.00 |