| Variant ID: vg0121065562 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 21065562 |
| 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: 313. )
TGACTCATAGTGGGAAAACCCTGAAGAAATTGGCATCAAAGAAAGATTCATTGCTGAAGAAAGTAGAAAAGACAGAATGTTGTACTACTATGGTGCTCTG[G/A]
GGGAAGAAGGAGGAAAATCTAGTCATAGAACAAGAGTCTCAGGAGATGGTGACACCGGTCGAGATGCAATCTCAAGATGAGGGAGGTGAAATGACAAATG
CATTTGTCATTTCACCTCCCTCATCTTGAGATTGCATCTCGACCGGTGTCACCATCTCCTGAGACTCTTGTTCTATGACTAGATTTTCCTCCTTCTTCCC[C/T]
CAGAGCACCATAGTAGTACAACATTCTGTCTTTTCTACTTTCTTCAGCAATGAATCTTTCTTTGATGCCAATTTCTTCAGGGTTTTCCCACTATGAGTCA
| 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% | 0.10% | 0.15% | 2.29% | NA |
| All Indica | 2759 | 99.50% | 0.10% | 0.07% | 0.33% | NA |
| All Japonica | 1512 | 93.30% | 0.00% | 0.26% | 6.42% | NA |
| Aus | 269 | 98.10% | 1.50% | 0.37% | 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 | 98.80% | 0.20% | 0.00% | 0.99% | NA |
| Indica Intermediate | 786 | 99.60% | 0.10% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 95.40% | 0.00% | 0.20% | 4.37% | NA |
| Japonica Intermediate | 241 | 68.90% | 0.00% | 1.24% | 29.88% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0121065562 | G -> A | LOC_Os01g37660.1 | stop_gained ; p.Trp34*; HIGH | stop_gained | Average:50.219; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 | N | N | N | N |
| vg0121065562 | G -> DEL | LOC_Os01g37660.1 | N | frameshift_variant | Average:50.219; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 | N | N | N | N |