| Variant ID: vg1220960884 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960884 |
| 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: 345. )
GGCTTTCCAAGGAATGGTGGGGTGAGGCAGTTTTGACTGCTTGTCATGTCCTGAATAAAATTCCAATGAAGCATAAGGAAGTAACACCATTCGAGGAATG[G/A]
GAAAGGAAGAAATTAAATCTCTCATACCTACGAACATGGGGCTGTTTGGCCAAGGTAAATGTACCTATAGCCAAAAAGCGGAAACTTGGACCAAAAACTG
CAGTTTTTGGTCCAAGTTTCCGCTTTTTGGCTATAGGTACATTTACCTTGGCCAAACAGCCCCATGTTCGTAGGTATGAGAGATTTAATTTCTTCCTTTC[C/T]
CATTCCTCGAATGGTGTTACTTCCTTATGCTTCATTGGAATTTTATTCAGGACATGACAAGCAGTCAAAACTGCCTCACCCCACCATTCCTTGGAAAGCC
| 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 | 3.20% | 2.80% | 21.69% | 72.32% | NA |
| All Indica | 2759 | 2.30% | 4.40% | 29.79% | 63.47% | NA |
| All Japonica | 1512 | 4.70% | 0.10% | 7.54% | 87.63% | NA |
| Aus | 269 | 4.50% | 2.20% | 25.28% | 68.03% | NA |
| Indica I | 595 | 0.00% | 3.00% | 20.34% | 76.64% | NA |
| Indica II | 465 | 3.90% | 3.90% | 32.04% | 60.22% | NA |
| Indica III | 913 | 2.80% | 6.40% | 35.05% | 55.75% | NA |
| Indica Intermediate | 786 | 2.50% | 3.60% | 29.52% | 64.38% | NA |
| Temperate Japonica | 767 | 0.30% | 0.00% | 5.08% | 94.65% | NA |
| Tropical Japonica | 504 | 6.00% | 0.40% | 11.90% | 81.75% | NA |
| Japonica Intermediate | 241 | 16.20% | 0.00% | 6.22% | 77.59% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 5.21% | 94.79% | NA |
| Intermediate | 90 | 4.40% | 2.20% | 17.78% | 75.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960884 | G -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg1220960884 | G -> A | LOC_Os12g34580.1 | stop_gained ; p.Trp756*; HIGH | stop_gained | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |