| Variant ID: vg0620602949 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20602949 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCACTAATTTAGTGCAGTCCGGACCAACCCTATCCTTACCCGAATATGTGCTACTGCAACATTTCCATATAGGTTTGGATAAGGAGTCTGCATTCTATCT[G/A]
GACATAACCGTCGGAGGATCGTTGATGCACAAAACGCCGTCGGAAGGAAGAACAATTTTGGATCATATTCTAGAAAATACTTCCTTCATGACGCAATCTG
CAGATTGCGTCATGAAGGAAGTATTTTCTAGAATATGATCCAAAATTGTTCTTCCTTCCGACGGCGTTTTGTGCATCAACGATCCTCCGACGGTTATGTC[C/T]
AGATAGAATGCAGACTCCTTATCCAAACCTATATGGAAATGTTGCAGTAGCACATATTCGGGTAAGGATAGGGTTGGTCCGGACTGCACTAAATTAGTGA
| 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 | 97.40% | 1.40% | 0.06% | 1.14% | NA |
| All Indica | 2759 | 99.60% | 0.20% | 0.07% | 0.07% | NA |
| All Japonica | 1512 | 96.30% | 0.40% | 0.00% | 3.31% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.30% | 0.11% | 0.11% | NA |
| Indica Intermediate | 786 | 99.50% | 0.30% | 0.13% | 0.13% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 98.40% | 0.60% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 82.60% | 1.20% | 0.00% | 16.18% | NA |
| VI/Aromatic | 96 | 49.00% | 51.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0620602949 | G -> A | LOC_Os06g35340.1 | synonymous_variant ; p.Leu131Leu; LOW | synonymous_codon | Average:12.573; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg0620602949 | G -> DEL | LOC_Os06g35340.1 | N | frameshift_variant | Average:12.573; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |