| Variant ID: vg0811599496 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599496 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGAGTCCAGTGCGCCCTGCGGCTCGGCGATGGTGTGTTCGGCGGCTGCGAGGCGGGCGGCTAGGTCGCCCTGGCCCGCGGCCGCCCCGCCGCTGTGCGCT[C/A]
TCGCGTCCAGCTCCTTCGCCCGCGCCTCGAGCTCAGCGGCCCGCTGATCCAGTGCGGCCCTCTCGGCGCGGACGCCTTCCAGATTGCGGCGCGCCTGCTC
GAGCAGGCGCGCCGCAATCTGGAAGGCGTCCGCGCCGAGAGGGCCGCACTGGATCAGCGGGCCGCTGAGCTCGAGGCGCGGGCGAAGGAGCTGGACGCGA[G/T]
AGCGCACAGCGGCGGGGCGGCCGCGGGCCAGGGCGACCTAGCCGCCCGCCTCGCAGCCGCCGAACACACCATCGCCGAGCCGCAGGGCGCACTGGACTCG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 1.40% | 0.10% | 15.09% | 83.37% | NA |
| All Indica | 2759 | 2.20% | 0.20% | 13.45% | 84.20% | NA |
| All Japonica | 1512 | 0.10% | 0.00% | 13.96% | 85.98% | NA |
| Aus | 269 | 1.90% | 0.00% | 33.83% | 64.31% | NA |
| Indica I | 595 | 1.30% | 0.00% | 6.22% | 92.44% | NA |
| Indica II | 465 | 0.00% | 0.00% | 5.16% | 94.84% | NA |
| Indica III | 913 | 4.20% | 0.50% | 24.32% | 70.97% | NA |
| Indica Intermediate | 786 | 1.80% | 0.00% | 11.20% | 87.02% | NA |
| Temperate Japonica | 767 | 0.00% | 0.00% | 10.04% | 89.96% | NA |
| Tropical Japonica | 504 | 0.20% | 0.00% | 21.23% | 78.57% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 11.20% | 88.80% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 27.08% | 71.88% | NA |
| Intermediate | 90 | 0.00% | 1.10% | 15.56% | 83.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599496 | C -> A | LOC_Os08g19400.1 | missense_variant ; p.Arg136Ile; MODERATE | nonsynonymous_codon ; R136I | Average:17.671; most accessible tissue: Zhenshan97 root, score: 30.989 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0811599496 | C -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:17.671; most accessible tissue: Zhenshan97 root, score: 30.989 | N | N | N | N |