| Variant ID: vg0905620954 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 5620954 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.01, others allele: 0.00, population size: 254. )
AAGAGATGGATCTTCTTCCTCTGGAATAGCTGGCAACGATCTAACGAGGCACTAATCCCGCCTTGCGTCGAAGCGAAGAGATGGATCTTCTTCCTCTGGA[A/G]
TAGCTGGCTCTCTTTCTTCTGGATCTTCCTCCTCTGGGGTAGCTGACGGCGGTGCTTCTCCCTTGAGCTCGGCCAGTTCCTTCTGCAGGCGATACACCTT
AAGGTGTATCGCCTGCAGAAGGAACTGGCCGAGCTCAAGGGAGAAGCACCGCCGTCAGCTACCCCAGAGGAGGAAGATCCAGAAGAAAGAGAGCCAGCTA[T/C]
TCCAGAGGAAGAAGATCCATCTCTTCGCTTCGACGCAAGGCGGGATTAGTGCCTCGTTAGATCGTTGCCAGCTATTCCAGAGGAAGAAGATCCATCTCTT
| 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 | 94.30% | 0.20% | 2.98% | 2.48% | NA |
| All Indica | 2759 | 94.60% | 0.20% | 3.55% | 1.63% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 56.90% | 1.50% | 15.61% | 26.02% | NA |
| Indica I | 595 | 93.60% | 0.70% | 4.54% | 1.18% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.43% | 0.00% | NA |
| Indica III | 913 | 95.00% | 0.10% | 2.96% | 1.97% | NA |
| Indica Intermediate | 786 | 92.00% | 0.10% | 5.34% | 2.54% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0905620954 | A -> G | LOC_Os09g10310.1 | missense_variant ; p.Ile192Thr; MODERATE | nonsynonymous_codon ; I192T | Average:53.558; most accessible tissue: Zhenshan97 flag leaf, score: 67.31 | unknown | unknown | TOLERATED | 1.00 |
| vg0905620954 | A -> DEL | LOC_Os09g10310.1 | N | frameshift_variant | Average:53.558; most accessible tissue: Zhenshan97 flag leaf, score: 67.31 | N | N | N | N |