| Variant ID: vg0620602260 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20602260 |
| Reference Allele: G | Alternative Allele: A,T |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CAGGTTTTGGCATGGATGCTCCAGATCACTCCCTGATGGCGGTTGGAGGGCACTTTGGACATTTCCCCTTCGCCAACCGTCATACCTACCGCTATATAAA[G/A,T]
ACATCACTCCCTCACTTCACTTACACACTTCCAAGCTTGAGCTGAATTATAAGAGGCTCTATTGTACTATATTGTATACTAGAATAGGAAGAGAGTAGAG
CTCTACTCTCTTCCTATTCTAGTATACAATATAGTACAATAGAGCCTCTTATAATTCAGCTCAAGCTTGGAAGTGTGTAAGTGAAGTGAGGGAGTGATGT[C/T,A]
TTTATATAGCGGTAGGTATGACGGTTGGCGAAGGGGAAATGTCCAAAGTGCCCTCCAACCGCCATCAGGGAGTGATCTGGAGCATCCATGCCAAAACCTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 81.70% | 16.00% | 0.11% | 1.16% | T: 0.99% |
| All Indica | 2759 | 97.20% | 1.10% | 0.07% | 0.07% | T: 1.63% |
| All Japonica | 1512 | 49.50% | 46.90% | 0.13% | 3.37% | T: 0.13% |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 95.70% | 2.60% | 0.22% | 0.00% | T: 1.51% |
| Indica III | 913 | 95.80% | 0.20% | 0.00% | 0.11% | T: 3.83% |
| Indica Intermediate | 786 | 97.60% | 1.90% | 0.00% | 0.13% | T: 0.38% |
| Temperate Japonica | 767 | 80.10% | 19.20% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 10.70% | 87.70% | 0.00% | 1.19% | T: 0.40% |
| Japonica Intermediate | 241 | 33.20% | 49.80% | 0.83% | 16.18% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 74.40% | 22.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0620602260 | 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 |
| vg0620602260 | G -> A | LOC_Os06g35340.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.088; most accessible tissue: Minghui63 flower, score: 10.335 | N | N | N | N |
| vg0620602260 | G -> DEL | N | N | silent_mutation | Average:6.088; most accessible tissue: Minghui63 flower, score: 10.335 | N | N | N | N |