| Variant ID: vg0234178709 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34178709 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 286. )
AACTACGTGTCGAGGTCATTCCCAACTGGTGAGTATGATGCCACCGGATCGGCTCCAACACCACCAGTTATGGAGCCACCGGCGGGTTCAGAAGCATCCG[G/A]
CACTATGAGTGGGAGTGCATCGACGAACACCGGCTCAAAGAGATCAAGAACTTCCGGTGTTTGGCAACATTTCGATGAGGTGGCCATGACAGGCCCTGAT
ATCAGGGCCTGTCATGGCCACCTCATCGAAATGTTGCCAAACACCGGAAGTTCTTGATCTCTTTGAGCCGGTGTTCGTCGATGCACTCCCACTCATAGTG[C/T]
CGGATGCTTCTGAACCCGCCGGTGGCTCCATAACTGGTGGTGTTGGAGCCGATCCGGTGGCATCATACTCACCAGTTGGGAATGACCTCGACACGTAGTT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 44.40% | 1.00% | 21.73% | 32.88% | NA |
| All Indica | 2759 | 16.80% | 1.50% | 31.10% | 50.60% | NA |
| All Japonica | 1512 | 94.50% | 0.00% | 3.37% | 2.12% | NA |
| Aus | 269 | 44.20% | 1.10% | 33.46% | 21.19% | NA |
| Indica I | 595 | 9.20% | 0.30% | 27.39% | 63.03% | NA |
| Indica II | 465 | 8.80% | 1.50% | 19.57% | 70.11% | NA |
| Indica III | 913 | 26.60% | 2.50% | 36.91% | 33.95% | NA |
| Indica Intermediate | 786 | 15.80% | 1.30% | 33.97% | 48.98% | NA |
| Temperate Japonica | 767 | 97.30% | 0.00% | 0.52% | 2.22% | NA |
| Tropical Japonica | 504 | 90.30% | 0.00% | 9.13% | 0.60% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 0.41% | 4.98% | NA |
| VI/Aromatic | 96 | 35.40% | 2.10% | 13.54% | 48.96% | NA |
| Intermediate | 90 | 58.90% | 0.00% | 16.67% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234178709 | G -> A | LOC_Os02g55830.1 | missense_variant ; p.Gly50Asp; MODERATE | nonsynonymous_codon ; G50N | Average:5.041; most accessible tissue: Minghui63 panicle, score: 16.27 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0234178709 | G -> DEL | LOC_Os02g55830.1 | N | frameshift_variant | Average:5.041; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |