| Variant ID: vg1201715500 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 1715500 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 99. )
TTCCGTCGAGGGGTGTACCAGGGAGAGGTGTACTGGGCTGGCCGAGTGATCAGGCCTCGTCCTTCGCCCATGCTAGGACGACGTCGCCGCGCCGCCGACG[G/T]
GGATGCCCCGATGCAAGATGTCGCGAGATGTCCTCCTGGGCCTCGCGCTGACGAAGGCGTGCGACGCGAGGCAGGAGGAGTGCGCCGTGTGCCTCAGGGA
TCCCTGAGGCACACGGCGCACTCCTCCTGCCTCGCGTCGCACGCCTTCGTCAGCGCGAGGCCCAGGAGGACATCTCGCGACATCTTGCATCGGGGCATCC[C/A]
CGTCGGCGGCGCGGCGACGTCGTCCTAGCATGGGCGAAGGACGAGGCCTGATCACTCGGCCAGCCCAGTACACCTCTCCCTGGTACACCCCTCGACGGAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.60% | 0.80% | 0.95% | 54.61% | NA |
| All Indica | 2759 | 7.90% | 1.40% | 1.45% | 89.31% | NA |
| All Japonica | 1512 | 97.20% | 0.00% | 0.00% | 2.84% | NA |
| Aus | 269 | 82.20% | 0.40% | 1.12% | 16.36% | NA |
| Indica I | 595 | 1.30% | 1.00% | 0.50% | 97.14% | NA |
| Indica II | 465 | 4.50% | 1.50% | 1.08% | 92.90% | NA |
| Indica III | 913 | 9.90% | 1.80% | 2.63% | 85.76% | NA |
| Indica Intermediate | 786 | 12.50% | 1.10% | 1.02% | 85.37% | NA |
| Temperate Japonica | 767 | 95.40% | 0.00% | 0.00% | 4.56% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 66.70% | 1.10% | 2.22% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1201715500 | G -> DEL | LOC_Os12g04090.1 | N | frameshift_variant | Average:70.815; most accessible tissue: Callus, score: 91.31 | N | N | N | N |
| vg1201715500 | G -> T | LOC_Os12g04090.1 | missense_variant ; p.Gly109Trp; MODERATE | nonsynonymous_codon ; G109W | Average:70.815; most accessible tissue: Callus, score: 91.31 | unknown | unknown | DELETERIOUS | 0.02 |