| Variant ID: vg0801635017 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 1635017 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTCGAGTCGTCGGCGTTCGTCCGCGACGACCGCCTCATCGTCGAGTGCGTCATCGACGTCGTCGTCGCCAACGGCGGCGACGACGACACGGCGGCCGCGG[C/A]
GTCCCCCCTCGCCGGCGTGCCGGCGCCGGACCTGTCGAGGCACCTCGGCGAGCTGCTGGAGCGGGCGGACGGCGTGGGCGCGGACGTCACGTTCGACGTC
GACGTCGAACGTGACGTCCGCGCCCACGCCGTCCGCCCGCTCCAGCAGCTCGCCGAGGTGCCTCGACAGGTCCGGCGCCGGCACGCCGGCGAGGGGGGAC[G/T]
CCGCGGCCGCCGTGTCGTCGTCGCCGCCGTTGGCGACGACGACGTCGATGACGCACTCGACGATGAGGCGGTCGTCGCGGACGAACGCCGACGACTCGAG
| 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 | 97.80% | 1.40% | 0.00% | 0.72% | NA |
| All Indica | 2759 | 96.30% | 2.50% | 0.00% | 1.23% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.60% | 0.00% | 0.00% | 2.35% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 93.00% | 6.20% | 0.00% | 0.77% | NA |
| Indica Intermediate | 786 | 96.90% | 1.40% | 0.00% | 1.65% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0801635017 | C -> A | LOC_Os08g03490.1 | missense_variant ; p.Ala172Glu; MODERATE | nonsynonymous_codon ; A172E | Average:74.791; most accessible tissue: Zhenshan97 root, score: 81.772 | unknown | unknown | TOLERATED | 1.00 |
| vg0801635017 | C -> DEL | LOC_Os08g03490.1 | N | frameshift_variant | Average:74.791; most accessible tissue: Zhenshan97 root, score: 81.772 | N | N | N | N |