| Variant ID: vg0620602250 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20602250 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CCGTTGATCCCAGGTTTTGGCATGGATGCTCCAGATCACTCCCTGATGGCGGTTGGAGGGCACTTTGGACATTTCCCCTTCGCCAACCGTCATACCTACC[G/T]
CTATATAAAGACATCACTCCCTCACTTCACTTACACACTTCCAAGCTTGAGCTGAATTATAAGAGGCTCTATTGTACTATATTGTATACTAGAATAGGAA
TTCCTATTCTAGTATACAATATAGTACAATAGAGCCTCTTATAATTCAGCTCAAGCTTGGAAGTGTGTAAGTGAAGTGAGGGAGTGATGTCTTTATATAG[C/A]
GGTAGGTATGACGGTTGGCGAAGGGGAAATGTCCAAAGTGCCCTCCAACCGCCATCAGGGAGTGATCTGGAGCATCCATGCCAAAACCTGGGATCAACGG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.50% | 13.10% | 0.13% | 1.25% | NA |
| All Indica | 2759 | 99.70% | 0.20% | 0.04% | 0.07% | NA |
| All Japonica | 1512 | 56.20% | 40.00% | 0.13% | 3.64% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.20% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 99.70% | 0.10% | 0.00% | 0.13% | NA |
| Temperate Japonica | 767 | 27.40% | 71.80% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 95.20% | 3.40% | 0.00% | 1.39% | NA |
| Japonica Intermediate | 241 | 66.40% | 15.40% | 0.83% | 17.43% | NA |
| VI/Aromatic | 96 | 96.90% | 1.00% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 10.00% | 1.11% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620602250 | G -> T | LOC_Os06g35340.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.088; most accessible tissue: Minghui63 flower, score: 10.335 | N | N | N | N |
| vg0620602250 | G -> DEL | N | N | silent_mutation | Average:6.088; most accessible tissue: Minghui63 flower, score: 10.335 | N | N | N | N |