| Variant ID: vg0121065536 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 21065536 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 345. )
TCCTACTTACATAGGGAAAACACAGATGACTCATAGTGGGAAAACCCTGAAGAAATTGGCATCAAAGAAAGATTCATTGCTGAAGAAAGTAGAAAAGACA[G/A]
AATGTTGTACTACTATGGTGCTCTGGGGGAAGAAGGAGGAAAATCTAGTCATAGAACAAGAGTCTCAGGAGATGGTGACACCGGTCGAGATGCAATCTCA
TGAGATTGCATCTCGACCGGTGTCACCATCTCCTGAGACTCTTGTTCTATGACTAGATTTTCCTCCTTCTTCCCCCAGAGCACCATAGTAGTACAACATT[C/T]
TGTCTTTTCTACTTTCTTCAGCAATGAATCTTTCTTTGATGCCAATTTCTTCAGGGTTTTCCCACTATGAGTCATCTGTGTTTTCCCTATGTAAGTAGGA
| 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 | 96.20% | 0.30% | 1.50% | 2.03% | NA |
| All Indica | 2759 | 99.40% | 0.00% | 0.62% | 0.00% | NA |
| All Japonica | 1512 | 89.70% | 0.70% | 3.37% | 6.22% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.20% | 0.00% | 1.78% | 0.00% | NA |
| Temperate Japonica | 767 | 94.50% | 0.90% | 4.17% | 0.39% | NA |
| Tropical Japonica | 504 | 94.20% | 0.00% | 1.39% | 4.37% | NA |
| Japonica Intermediate | 241 | 64.70% | 1.70% | 4.98% | 28.63% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0121065536 | G -> A | LOC_Os01g37660.1 | missense_variant ; p.Glu26Lys; MODERATE | nonsynonymous_codon ; E26K | Average:49.703; most accessible tissue: Zhenshan97 flag leaf, score: 78.761 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0121065536 | G -> DEL | LOC_Os01g37660.1 | N | frameshift_variant | Average:49.703; most accessible tissue: Zhenshan97 flag leaf, score: 78.761 | N | N | N | N |