| Variant ID: vg0620603060 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20603060 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCGGAGGATCGTTGATGCACAAAACGCCGTCGGAAGGAAGAACAATTTTGGATCATATTCTAGAAAATACTTCCTTCATGACGCAATCTGATGAACCCCA[A/G]
CCGGAGGCATACGTGTCCAAAATAGAGGAACCTCTAACGATCGAGCCGCTCACTGAACCATCCACTTCTGCTAGCTCGATTGATGAGAAGGTTGCTAAGC
GCTTAGCAACCTTCTCATCAATCGAGCTAGCAGAAGTGGATGGTTCAGTGAGCGGCTCGATCGTTAGAGGTTCCTCTATTTTGGACACGTATGCCTCCGG[T/C]
TGGGGTTCATCAGATTGCGTCATGAAGGAAGTATTTTCTAGAATATGATCCAAAATTGTTCTTCCTTCCGACGGCGTTTTGTGCATCAACGATCCTCCGA
| 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 | 85.50% | 13.20% | 0.11% | 1.23% | NA |
| All Indica | 2759 | 99.60% | 0.30% | 0.04% | 0.07% | NA |
| All Japonica | 1512 | 56.30% | 40.00% | 0.13% | 3.57% | 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 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 99.40% | 0.40% | 0.13% | 0.13% | NA |
| Temperate Japonica | 767 | 27.40% | 71.70% | 0.13% | 0.78% | NA |
| Tropical Japonica | 504 | 95.20% | 3.60% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 66.80% | 15.40% | 0.41% | 17.43% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 83.30% | 12.20% | 2.22% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620603060 | A -> G | LOC_Os06g35340.1 | synonymous_variant ; p.Gln168Gln; LOW | synonymous_codon | Average:10.028; most accessible tissue: Minghui63 flag leaf, score: 14.81 | N | N | N | N |
| vg0620603060 | A -> DEL | LOC_Os06g35340.1 | N | frameshift_variant | Average:10.028; most accessible tissue: Minghui63 flag leaf, score: 14.81 | N | N | N | N |