| Variant ID: vg0527589254 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 27589254 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 103. )
AGATGCAGCGGTCGTCCCCTTCCTCTCGGTCGCAGGGGTCGGCGTCGGTGTTGCTCCAGGCAGCGATGCAGCGGCCATGCCCTTCCTCTCAGGTGCAGGC[G/A]
CCGGCGTTGCTCCAAGCGGCGATGCAGCCGCCGTCCTCTTCCTCGCAGGCGTCGGCGTCGGCGTTGTTCCAGGGGGCGCCCGCACGTCGACCACCGCCTC
GAGGCGGTGGTCGACGTGCGGGCGCCCCCTGGAACAACGCCGACGCCGACGCCTGCGAGGAAGAGGACGGCGGCTGCATCGCCGCTTGGAGCAACGCCGG[C/T]
GCCTGCACCTGAGAGGAAGGGCATGGCCGCTGCATCGCTGCCTGGAGCAACACCGACGCCGACCCCTGCGACCGAGAGGAAGGGGACGACCGCTGCATCT
| 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 | 80.00% | 11.20% | 6.62% | 2.18% | NA |
| All Indica | 2759 | 66.90% | 18.90% | 10.69% | 3.52% | NA |
| All Japonica | 1512 | 99.00% | 0.10% | 0.66% | 0.26% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 61.30% | 6.10% | 25.38% | 7.23% | NA |
| Indica II | 465 | 53.80% | 32.90% | 10.11% | 3.23% | NA |
| Indica III | 913 | 76.50% | 20.20% | 1.97% | 1.42% | NA |
| Indica Intermediate | 786 | 67.70% | 19.00% | 10.05% | 3.31% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 97.60% | 0.20% | 1.59% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 5.60% | 7.78% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0527589254 | G -> DEL | LOC_Os05g48130.1 | N | frameshift_variant | Average:28.394; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0527589254 | G -> A | LOC_Os05g48130.1 | synonymous_variant ; p.Ala33Ala; LOW | synonymous_codon | Average:28.394; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |