| Variant ID: vg0811599474 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599474 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GGGCCTCGACCTCCCCGGCGGACGAGTCCAGTGCGCCCTGCGGCTCGGCGATGGTGTGTTCGGCGGCTGCGAGGCGGGCGGCTAGGTCGCCCTGGCCCGC[G/A]
GCCGCCCCGCCGCTGTGCGCTCTCGCGTCCAGCTCCTTCGCCCGCGCCTCGAGCTCAGCGGCCCGCTGATCCAGTGCGGCCCTCTCGGCGCGGACGCCTT
AAGGCGTCCGCGCCGAGAGGGCCGCACTGGATCAGCGGGCCGCTGAGCTCGAGGCGCGGGCGAAGGAGCTGGACGCGAGAGCGCACAGCGGCGGGGCGGC[C/T]
GCGGGCCAGGGCGACCTAGCCGCCCGCCTCGCAGCCGCCGAACACACCATCGCCGAGCCGCAGGGCGCACTGGACTCGTCCGCCGGGGAGGTCGAGGCCC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.10% | 0.10% | 4.27% | 95.49% | NA |
| All Indica | 2759 | 0.30% | 0.10% | 3.66% | 96.01% | NA |
| All Japonica | 1512 | 0.00% | 0.10% | 5.75% | 94.18% | NA |
| Aus | 269 | 0.00% | 0.40% | 4.46% | 95.17% | NA |
| Indica I | 595 | 0.00% | 0.00% | 0.34% | 99.66% | NA |
| Indica II | 465 | 0.00% | 0.00% | 0.65% | 99.35% | NA |
| Indica III | 913 | 0.50% | 0.00% | 9.20% | 90.25% | NA |
| Indica Intermediate | 786 | 0.30% | 0.30% | 1.53% | 97.96% | NA |
| Temperate Japonica | 767 | 0.00% | 0.10% | 7.30% | 92.57% | NA |
| Tropical Japonica | 504 | 0.00% | 0.00% | 3.97% | 96.03% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 4.56% | 95.44% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 2.22% | 97.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599474 | G -> A | LOC_Os08g19400.1 | synonymous_variant ; p.Ala143Ala; LOW | nonsynonymous_codon ; A143T | Average:20.16; most accessible tissue: Zhenshan97 root, score: 32.766 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0811599474 | G -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:20.16; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |