| Variant ID: vg1012223908 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12223908 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.60, T: 0.40, others allele: 0.00, population size: 35. )
ATCACACCAAAAAAAAAAAATATCAGGGAGCAGCCGCCGCCGACGAGGTTGTCCACGGCAAGGGAGCGGGTAGCGGCGACCGCGCGCCAGGAGCGACCAA[T/C]
GGCGCGGATGCGGACACGGTCGGGGAGGGAGCGCGAGGACGGCGGCGTGGAGCGTGAGCAGGAGGCGGCTGCGCGCAAGGCCGGCAACGGCGGTGCGGAG
CTCCGCACCGCCGTTGCCGGCCTTGCGCGCAGCCGCCTCCTGCTCACGCTCCACGCCGCCGTCCTCGCGCTCCCTCCCCGACCGTGTCCGCATCCGCGCC[A/G]
TTGGTCGCTCCTGGCGCGCGGTCGCCGCTACCCGCTCCCTTGCCGTGGACAACCTCGTCGGCGGCGGCTGCTCCCTGATATTTTTTTTTTTTGGTGTGAT
| 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 | 30.60% | 17.70% | 1.71% | 50.00% | NA |
| All Indica | 2759 | 2.30% | 28.50% | 2.25% | 66.91% | NA |
| All Japonica | 1512 | 88.00% | 0.50% | 0.40% | 11.11% | NA |
| Aus | 269 | 0.70% | 10.00% | 2.97% | 86.25% | NA |
| Indica I | 595 | 3.00% | 7.20% | 3.53% | 86.22% | NA |
| Indica II | 465 | 3.00% | 35.90% | 2.80% | 58.28% | NA |
| Indica III | 913 | 0.90% | 33.80% | 1.75% | 63.53% | NA |
| Indica Intermediate | 786 | 3.10% | 34.10% | 1.53% | 61.32% | NA |
| Temperate Japonica | 767 | 95.30% | 0.30% | 0.13% | 4.30% | NA |
| Tropical Japonica | 504 | 81.30% | 0.40% | 0.40% | 17.86% | NA |
| Japonica Intermediate | 241 | 78.80% | 1.20% | 1.24% | 18.67% | NA |
| VI/Aromatic | 96 | 6.20% | 3.10% | 4.17% | 86.46% | NA |
| Intermediate | 90 | 45.60% | 15.60% | 1.11% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012223908 | T -> C | LOC_Os10g23830.1 | start_lost ; p.Met1?; HIGH | nonsynonymous_codon ; M1T | Average:8.866; most accessible tissue: Callus, score: 26.513 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1012223908 | T -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:8.866; most accessible tissue: Callus, score: 26.513 | N | N | N | N |