| Variant ID: vg0915034277 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 15034277 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGTCAACGGCTTCGAGGGCTCGGCCCCTCGGCTCGCGTTCGCCCCCGACTCCGACGAGGAGGGGAACGCCAGCAGTGCAAGCGACGGTGGCAACGAGGCC[G/A]
GCGACCTGGGCGCGTCAGAATGAGCCCCCAGGCCCCCGCCCATCTTAACTTTTTTCTTTTTCTTTCTTCTAAGGCCTTCATGCCTCTTTTTTGTACAAAT
ATTTGTACAAAAAAGAGGCATGAAGGCCTTAGAAGAAAGAAAAAGAAAAAAGTTAAGATGGGCGGGGGCCTGGGGGCTCATTCTGACGCGCCCAGGTCGC[C/T]
GGCCTCGTTGCCACCGTCGCTTGCACTGCTGGCGTTCCCCTCCTCGTCGGAGTCGGGGGCGAACGCGAGCCGAGGGGCCGAGCCCTCGAAGCCGTTGACG
| 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 | 17.80% | 0.10% | 8.32% | 73.78% | NA |
| All Indica | 2759 | 3.40% | 0.10% | 10.73% | 85.79% | NA |
| All Japonica | 1512 | 43.40% | 0.00% | 3.37% | 53.24% | NA |
| Aus | 269 | 20.40% | 0.00% | 6.69% | 72.86% | NA |
| Indica I | 595 | 3.70% | 0.00% | 7.23% | 89.08% | NA |
| Indica II | 465 | 3.20% | 0.00% | 9.25% | 87.53% | NA |
| Indica III | 913 | 3.30% | 0.20% | 12.49% | 84.01% | NA |
| Indica Intermediate | 786 | 3.30% | 0.10% | 12.21% | 84.35% | NA |
| Temperate Japonica | 767 | 68.20% | 0.00% | 0.78% | 31.03% | NA |
| Tropical Japonica | 504 | 10.50% | 0.00% | 4.96% | 84.52% | NA |
| Japonica Intermediate | 241 | 33.20% | 0.00% | 8.30% | 58.51% | NA |
| VI/Aromatic | 96 | 12.50% | 2.10% | 15.62% | 69.79% | NA |
| Intermediate | 90 | 27.80% | 0.00% | 14.44% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0915034277 | G -> DEL | LOC_Os09g25110.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0915034277 | G -> A | LOC_Os09g25110.1 | missense_variant ; p.Gly964Ser; MODERATE | nonsynonymous_codon ; G964S | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 0.05 |