| Variant ID: vg0409081379 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9081379 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGCTTGTGAGAGGAGCAGGTGATGGCGGTGACCATCGTGGGAGGAGCAGGAGATGGCAGCAACGCTCCGTGGTGCTGGTGGGGAGATCTTCTGGCAACGA[C/T]
GGCAGTGCTCGCGAGCACGCGTGGATTCGACGAGGGTGGCTGCGGCGACGCTCGCGGACGCATTGGGGGTGACAGCAGCACTCGCGGGCACATCCAACAA
TTGTTGGATGTGCCCGCGAGTGCTGCTGTCACCCCCAATGCGTCCGCGAGCGTCGCCGCAGCCACCCTCGTCGAATCCACGCGTGCTCGCGAGCACTGCC[G/A]
TCGTTGCCAGAAGATCTCCCCACCAGCACCACGGAGCGTTGCTGCCATCTCCTGCTCCTCCCACGATGGTCACCGCCATCACCTGCTCCTCTCACAAGCA
| 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 | 96.40% | 2.90% | 0.76% | 0.00% | NA |
| All Indica | 2759 | 94.40% | 4.50% | 1.05% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.20% | 0.07% | 0.00% | NA |
| Aus | 269 | 98.10% | 1.10% | 0.74% | 0.00% | NA |
| Indica I | 595 | 95.30% | 2.90% | 1.85% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.20% | 0.43% | 0.00% | NA |
| Indica III | 913 | 93.20% | 6.60% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 92.20% | 6.00% | 1.78% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 5.60% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409081379 | C -> T | LOC_Os04g16690.1 | missense_variant ; p.Arg17Trp; MODERATE | nonsynonymous_codon ; R17W | Average:70.804; most accessible tissue: Zhenshan97 young leaf, score: 87.153 | unknown | unknown | DELETERIOUS | 0.00 |