| Variant ID: vg0801635304 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 1635304 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCACCGCGCGCCGCGGATCGCCGTCGACGACATGGAGCCGGAGGTGTTCGACGCGCTCCTCCGCTTCGTCTACAGCGACACGCTGGCGCTCCCCGGCGAC[C/T]
TCGGGGAAGGCGAGTACAAGGAGATGGTGCGGCAGCTGCTGGAGGCGGCCGACCGGTACGCCATGGACAGGCTCAGGGTGATCTGCGAGCTCATCCTCTC
GAGAGGATGAGCTCGCAGATCACCCTGAGCCTGTCCATGGCGTACCGGTCGGCCGCCTCCAGCAGCTGCCGCACCATCTCCTTGTACTCGCCTTCCCCGA[G/A]
GTCGCCGGGGAGCGCCAGCGTGTCGCTGTAGACGAAGCGGAGGAGCGCGTCGAACACCTCCGGCTCCATGTCGTCGACGGCGATCCGCGGCGCGCGGTGC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.70% | 1.60% | 0.00% | 0.70% | NA |
| All Indica | 2759 | 96.20% | 2.60% | 0.00% | 1.20% | 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 | 92.70% | 6.70% | 0.00% | 0.66% | NA |
| Indica Intermediate | 786 | 96.80% | 1.50% | 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 | 99.00% | 1.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0801635304 | C -> T | LOC_Os08g03490.1 | missense_variant ; p.Leu268Phe; MODERATE | nonsynonymous_codon ; L268F | Average:78.551; most accessible tissue: Zhenshan97 root, score: 84.358 | unknown | unknown | TOLERATED | 0.05 |
| vg0801635304 | C -> DEL | LOC_Os08g03490.1 | N | frameshift_variant | Average:78.551; most accessible tissue: Zhenshan97 root, score: 84.358 | N | N | N | N |