| Variant ID: vg1206299767 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 6299767 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.62, C: 0.36, others allele: 0.00, population size: 45. )
TAGTACGCGATGGGCATGGATATTGGCCTGGATTGCAGGTCGGATACGGAGTCGGAAGCTGTCCACTTTGAAGCAACACCCTCGCGGCGGAGGCCATCGC[C/T]
GGCGCCTCCAGCAGCGCTGCCGCCAAGACGAACATCATCATGACGAGCACCTCCGCCAGCCGCCGGCCGCCGGTGGTCCTGAGCGCCGCCGCCATCGCCG
CGGCGATGGCGGCGGCGCTCAGGACCACCGGCGGCCGGCGGCTGGCGGAGGTGCTCGTCATGATGATGTTCGTCTTGGCGGCAGCGCTGCTGGAGGCGCC[G/A]
GCGATGGCCTCCGCCGCGAGGGTGTTGCTTCAAAGTGGACAGCTTCCGACTCCGTATCCGACCTGCAATCCAGGCCAATATCCATGCCCATCGCGTACTA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 21.50% | 12.70% | 0.30% | 65.49% | NA |
| All Indica | 2759 | 27.50% | 1.40% | 0.04% | 71.11% | NA |
| All Japonica | 1512 | 9.50% | 34.70% | 0.79% | 54.96% | NA |
| Aus | 269 | 2.20% | 9.30% | 0.37% | 88.10% | NA |
| Indica I | 595 | 73.90% | 1.50% | 0.00% | 24.54% | NA |
| Indica II | 465 | 18.30% | 1.70% | 0.00% | 80.00% | NA |
| Indica III | 913 | 2.60% | 0.80% | 0.00% | 96.60% | NA |
| Indica Intermediate | 786 | 26.60% | 1.80% | 0.13% | 71.50% | NA |
| Temperate Japonica | 767 | 15.40% | 38.10% | 1.43% | 45.11% | NA |
| Tropical Japonica | 504 | 2.60% | 22.80% | 0.20% | 74.40% | NA |
| Japonica Intermediate | 241 | 5.40% | 49.00% | 0.00% | 45.64% | NA |
| VI/Aromatic | 96 | 85.40% | 0.00% | 0.00% | 14.58% | NA |
| Intermediate | 90 | 31.10% | 12.20% | 0.00% | 56.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1206299767 | C -> DEL | LOC_Os12g11610.1 | N | frameshift_variant | Average:63.886; most accessible tissue: Zhenshan97 panicle, score: 79.799 | N | N | N | N |
| vg1206299767 | C -> T | LOC_Os12g11610.1 | synonymous_variant ; p.Pro32Pro; LOW | synonymous_codon | Average:63.886; most accessible tissue: Zhenshan97 panicle, score: 79.799 | N | N | N | N |