| Variant ID: vg0121065569 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 21065569 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.02, others allele: 0.00, population size: 272. )
TAGTGGGAAAACCCTGAAGAAATTGGCATCAAAGAAAGATTCATTGCTGAAGAAAGTAGAAAAGACAGAATGTTGTACTACTATGGTGCTCTGGGGGAAG[A/G]
AGGAGGAAAATCTAGTCATAGAACAAGAGTCTCAGGAGATGGTGACACCGGTCGAGATGCAATCTCAAGATGAGGGAGGTGAAATGACAAATGAGAAGCT
AGCTTCTCATTTGTCATTTCACCTCCCTCATCTTGAGATTGCATCTCGACCGGTGTCACCATCTCCTGAGACTCTTGTTCTATGACTAGATTTTCCTCCT[T/C]
CTTCCCCCAGAGCACCATAGTAGTACAACATTCTGTCTTTTCTACTTTCTTCAGCAATGAATCTTTCTTTGATGCCAATTTCTTCAGGGTTTTCCCACTA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.00% | 0.80% | 0.08% | 2.16% | NA |
| All Indica | 2759 | 98.90% | 1.10% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 93.20% | 0.00% | 0.20% | 6.61% | NA |
| Aus | 269 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.70% | 1.10% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 95.20% | 0.00% | 0.00% | 4.76% | NA |
| Japonica Intermediate | 241 | 68.50% | 0.00% | 1.24% | 30.29% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0121065569 | A -> G | LOC_Os01g37660.1 | missense_variant ; p.Lys37Glu; MODERATE | nonsynonymous_codon ; K37E | Average:50.724; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0121065569 | A -> DEL | LOC_Os01g37660.1 | N | frameshift_variant | Average:50.724; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 | N | N | N | N |