| Variant ID: vg0420972720 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20972720 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 259. )
AAACCATGAAAGTGGAGAGAGCTCCTCCGGAGCTGAGGACTGTGCAAGCATTGGAAGCAATAAACGAAGCAGTTGTAGGGCAAGAACTCATGGATGTCGA[C/T]
GATGCTGGCGACCAAGAGGATGAAGGGTATGATGATGATCCCGTGGAGGCTGATGATGGTGGCGGCGATGACTAACCATTCACTACCACATAGAGGTATG
CATACCTCTATGTGGTAGTGAATGGTTAGTCATCGCCGCCACCATCATCAGCCTCCACGGGATCATCATCATACCCTTCATCCTCTTGGTCGCCAGCATC[G/A]
TCGACATCCATGAGTTCTTGCCCTACAACTGCTTCGTTTATTGCTTCCAATGCTTGCACAGTCCTCAGCTCCGGAGGAGCTCTCTCCACTTTCATGGTTT
| 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 | 95.90% | 1.40% | 2.71% | 0.06% | NA |
| All Indica | 2759 | 93.10% | 2.30% | 4.60% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.07% | 0.20% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.50% | 0.70% | 1.85% | 0.00% | NA |
| Indica II | 465 | 86.50% | 3.40% | 10.11% | 0.00% | NA |
| Indica III | 913 | 91.80% | 3.40% | 4.82% | 0.00% | NA |
| Indica Intermediate | 786 | 95.20% | 1.70% | 3.18% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420972720 | C -> DEL | LOC_Os04g34670.1 | N | frameshift_variant | Average:6.828; most accessible tissue: Zhenshan97 flower, score: 14.863 | N | N | N | N |
| vg0420972720 | C -> T | LOC_Os04g34670.1 | synonymous_variant ; p.Asp738Asp; LOW | synonymous_codon | Average:6.828; most accessible tissue: Zhenshan97 flower, score: 14.863 | N | N | N | N |