| Variant ID: vg1201715507 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 1715507 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 99. )
GAGGGGTGTACCAGGGAGAGGTGTACTGGGCTGGCCGAGTGATCAGGCCTCGTCCTTCGCCCATGCTAGGACGACGTCGCCGCGCCGCCGACGGGGATGC[C/T]
CCGATGCAAGATGTCGCGAGATGTCCTCCTGGGCCTCGCGCTGACGAAGGCGTGCGACGCGAGGCAGGAGGAGTGCGCCGTGTGCCTCAGGGACTTCGAG
CTCGAAGTCCCTGAGGCACACGGCGCACTCCTCCTGCCTCGCGTCGCACGCCTTCGTCAGCGCGAGGCCCAGGAGGACATCTCGCGACATCTTGCATCGG[G/A]
GCATCCCCGTCGGCGGCGCGGCGACGTCGTCCTAGCATGGGCGAAGGACGAGGCCTGATCACTCGGCCAGCCCAGTACACCTCTCCCTGGTACACCCCTC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.50% | 0.80% | 0.99% | 54.76% | NA |
| All Indica | 2759 | 7.60% | 1.30% | 1.67% | 89.38% | NA |
| All Japonica | 1512 | 97.20% | 0.10% | 0.00% | 2.78% | NA |
| Aus | 269 | 82.20% | 0.00% | 0.37% | 17.47% | NA |
| Indica I | 595 | 1.30% | 0.00% | 1.18% | 97.48% | NA |
| Indica II | 465 | 4.30% | 1.30% | 1.29% | 93.12% | NA |
| Indica III | 913 | 9.50% | 2.40% | 1.75% | 86.31% | NA |
| Indica Intermediate | 786 | 12.20% | 1.00% | 2.16% | 84.61% | NA |
| Temperate Japonica | 767 | 95.40% | 0.10% | 0.00% | 4.43% | 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% | 0.00% | 0.00% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1201715507 | C -> DEL | LOC_Os12g04090.1 | N | frameshift_variant | Average:70.261; most accessible tissue: Callus, score: 91.31 | N | N | N | N |
| vg1201715507 | C -> T | LOC_Os12g04090.1 | missense_variant ; p.Pro111Leu; MODERATE | nonsynonymous_codon ; P111V | Average:70.261; most accessible tissue: Callus, score: 91.31 | unknown | unknown | TOLERATED | 0.09 |