| Variant ID: vg0611474672 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 11474672 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCCCTTAGATCTACCAGATTGCTTGTTGGAGATGACACAGCAGTCCTCGAGCTCACCGAAGAGGGAGAACGCAAAGTGGAGGTCGTCGGCTTCGGCGCCC[C/T]
AGCCGAGGCCGTGGACGAAGAGCTTCATGCTCGTGAGGTCGGCCTCCGTTGCACATAGCACAACCGCCATCGTCGCAGGGGTCGTCATCGCGGTCGTGAG
CTCACGACCGCGATGACGACCCCTGCGACGATGGCGGTTGTGCTATGTGCAACGGAGGCCGACCTCACGAGCATGAAGCTCTTCGTCCACGGCCTCGGCT[G/A]
GGGCGCCGAAGCCGACGACCTCCACTTTGCGTTCTCCCTCTTCGGTGAGCTCGAGGACTGCTGTGTCATCTCCAACAAGCAATCTGGTAGATCTAAGGGC
| 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 | 98.10% | 1.20% | 0.66% | 0.00% | NA |
| All Indica | 2759 | 99.80% | 0.20% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 95.20% | 3.10% | 1.72% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.80% | 0.00% | 1.17% | 0.00% | NA |
| Tropical Japonica | 504 | 90.30% | 8.30% | 1.39% | 0.00% | NA |
| Japonica Intermediate | 241 | 93.80% | 2.10% | 4.15% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 6.70% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0611474672 | C -> T | LOC_Os06g20010.1 | stop_gained ; p.Trp24*; HIGH | stop_gained | Average:73.256; most accessible tissue: Zhenshan97 young leaf, score: 90.728 | N | N | N | N |