| Variant ID: vg0801634993 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 1634993 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGCGCGTTCATGCGGCGGCGCGACCTCGAGTCGTCGGCGTTCGTCCGCGACGACCGCCTCATCGTCGAGTGCGTCATCGACGTCGTCGTCGCCAACGGCG[G/A]
CGACGACGACACGGCGGCCGCGGCGTCCCCCCTCGCCGGCGTGCCGGCGCCGGACCTGTCGAGGCACCTCGGCGAGCTGCTGGAGCGGGCGGACGGCGTG
CACGCCGTCCGCCCGCTCCAGCAGCTCGCCGAGGTGCCTCGACAGGTCCGGCGCCGGCACGCCGGCGAGGGGGGACGCCGCGGCCGCCGTGTCGTCGTCG[C/T]
CGCCGTTGGCGACGACGACGTCGATGACGCACTCGACGATGAGGCGGTCGTCGCGGACGAACGCCGACGACTCGAGGTCGCGCCGCCGCATGAACGCGCG
| 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 | 94.00% | 5.30% | 0.00% | 0.72% | NA |
| All Indica | 2759 | 97.60% | 1.10% | 0.00% | 1.23% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 20.10% | 79.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.60% | 0.00% | 0.00% | 2.35% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.40% | 0.90% | 0.00% | 0.77% | NA |
| Indica Intermediate | 786 | 95.50% | 2.80% | 0.00% | 1.65% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0801634993 | G -> A | LOC_Os08g03490.1 | missense_variant ; p.Gly164Asp; MODERATE | nonsynonymous_codon ; G164D | Average:76.035; most accessible tissue: Zhenshan97 root, score: 82.361 | unknown | unknown | TOLERATED | 0.63 |
| vg0801634993 | G -> DEL | LOC_Os08g03490.1 | N | frameshift_variant | Average:76.035; most accessible tissue: Zhenshan97 root, score: 82.361 | N | N | N | N |