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Detailed information for vg0512045434:
| Variant ID: vg0512045434 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12045434 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 245. )
Flanking Sequence (100 bp) in Reference Genome:
TGCGGTAAGACGAATCCTGGCCTTCTGCGGCGGTGCTTCTCCCTTCAATGCGGCTAATTCCTTCTCCAAACGATCCACCTTGTCTTCTAGCTTGCAAATC[T/C]
TACCACGATTCCGGTCTTCACGATCTTGAGCGGCTAACACAGTCTCCGCACGACTTTCATCCATAGCCCACAACATCTCAACCAAATGCTTCGTGGTAGC
Reverse complement sequence
GCTACCACGAAGCATTTGGTTGAGATGTTGTGGGCTATGGATGAAAGTCGTGCGGAGACTGTGTTAGCCGCTCAAGATCGTGAAGACCGGAATCGTGGTA[A/G]
GATTTGCAAGCTAGAAGACAAGGTGGATCGTTTGGAGAAGGAATTAGCCGCATTGAAGGGAGAAGCACCGCCGCAGAAGGCCAGGATTCGTCTTACCGCA
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 | 82.10% | 1.40% | 6.47% | 10.05% | NA |
| All Indica | 2759 | 85.80% | 2.30% | 8.99% | 2.90% | NA |
| All Japonica | 1512 | 84.90% | 0.10% | 3.17% | 11.90% | NA |
| Aus | 269 | 22.30% | 0.00% | 0.37% | 77.32% | NA |
| Indica I | 595 | 91.40% | 0.50% | 8.07% | 0.00% | NA |
| Indica II | 465 | 97.60% | 0.00% | 0.86% | 1.51% | NA |
| Indica III | 913 | 76.20% | 5.40% | 13.80% | 4.60% | NA |
| Indica Intermediate | 786 | 85.60% | 1.50% | 8.91% | 3.94% | NA |
| Temperate Japonica | 767 | 72.50% | 0.00% | 5.61% | 21.90% | NA |
| Tropical Japonica | 504 | 99.20% | 0.20% | 0.20% | 0.40% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.00% | 1.66% | 4.15% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 84.40% | 2.20% | 6.67% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512045434 | T -> DEL | LOC_Os05g20520.1 | N | frameshift_variant | Average:15.294; most accessible tissue: Zhenshan97 flower, score: 25.98 | N | N | N | N |
| vg0512045434 | T -> C | LOC_Os05g20520.1 | missense_variant ; p.Lys183Arg; MODERATE | nonsynonymous_codon ; K183R | Average:15.294; most accessible tissue: Zhenshan97 flower, score: 25.98 | possibly damaging  |
1.503 |
DELETERIOUS | 0.02 |