| Variant ID: vg0121065598 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 21065598 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 300. )
CAAAGAAAGATTCATTGCTGAAGAAAGTAGAAAAGACAGAATGTTGTACTACTATGGTGCTCTGGGGGAAGAAGGAGGAAAATCTAGTCATAGAACAAGA[G/A]
TCTCAGGAGATGGTGACACCGGTCGAGATGCAATCTCAAGATGAGGGAGGTGAAATGACAAATGAGAAGCTATTAATGCATGAATGTTCCCCAACTGATG
CATCAGTTGGGGAACATTCATGCATTAATAGCTTCTCATTTGTCATTTCACCTCCCTCATCTTGAGATTGCATCTCGACCGGTGTCACCATCTCCTGAGA[C/T]
TCTTGTTCTATGACTAGATTTTCCTCCTTCTTCCCCCAGAGCACCATAGTAGTACAACATTCTGTCTTTTCTACTTTCTTCAGCAATGAATCTTTCTTTG
| 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 | 96.50% | 1.30% | 0.11% | 2.09% | NA |
| All Indica | 2759 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 93.30% | 0.00% | 0.33% | 6.42% | NA |
| Aus | 269 | 88.80% | 11.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 95.20% | 0.00% | 0.20% | 4.56% | NA |
| Japonica Intermediate | 241 | 68.90% | 0.00% | 1.66% | 29.46% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 1.10% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0121065598 | G -> A | LOC_Os01g37660.1 | synonymous_variant ; p.Glu46Glu; LOW | synonymous_codon | Average:45.175; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 | N | N | N | N |
| vg0121065598 | G -> DEL | LOC_Os01g37660.1 | N | frameshift_variant | Average:45.175; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 | N | N | N | N |