| Variant ID: vg1012224002 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12224002 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GACCAATGGCGCGGATGCGGACACGGTCGGGGAGGGAGCGCGAGGACGGCGGCGTGGAGCGTGAGCAGGAGGCGGCTGCGCGCAAGGCCGGCAACGGCGG[T/C]
GCGGAGCGCGAGCAGGATGTGGCCGTGCGCGAGAAGGCTGTTGAACGCTGGCCGGTACGAGGCTTGCTGCGGCCGCTGGTCGCTGGGTCTCGCCGGTATA
TATACCGGCGAGACCCAGCGACCAGCGGCCGCAGCAAGCCTCGTACCGGCCAGCGTTCAACAGCCTTCTCGCGCACGGCCACATCCTGCTCGCGCTCCGC[A/G]
CCGCCGTTGCCGGCCTTGCGCGCAGCCGCCTCCTGCTCACGCTCCACGCCGCCGTCCTCGCGCTCCCTCCCCGACCGTGTCCGCATCCGCGCCATTGGTC
| 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 | 49.00% | 0.20% | 1.21% | 49.62% | NA |
| All Indica | 2759 | 32.00% | 0.20% | 1.67% | 66.15% | NA |
| All Japonica | 1512 | 88.50% | 0.10% | 0.00% | 11.38% | NA |
| Aus | 269 | 11.20% | 0.70% | 2.60% | 85.50% | NA |
| Indica I | 595 | 12.30% | 0.30% | 2.18% | 85.21% | NA |
| Indica II | 465 | 40.00% | 0.00% | 2.15% | 57.85% | NA |
| Indica III | 913 | 35.80% | 0.30% | 1.31% | 62.54% | NA |
| Indica Intermediate | 786 | 37.70% | 0.10% | 1.40% | 60.81% | NA |
| Temperate Japonica | 767 | 95.60% | 0.00% | 0.00% | 4.43% | NA |
| Tropical Japonica | 504 | 81.90% | 0.00% | 0.00% | 18.06% | NA |
| Japonica Intermediate | 241 | 79.70% | 0.80% | 0.00% | 19.50% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 2.08% | 88.54% | NA |
| Intermediate | 90 | 61.10% | 0.00% | 2.22% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012224002 | T -> C | LOC_Os10g23830.1 | synonymous_variant ; p.Gly32Gly; LOW | synonymous_codon | Average:13.424; most accessible tissue: Callus, score: 51.074 | N | N | N | N |
| vg1012224002 | T -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:13.424; most accessible tissue: Callus, score: 51.074 | N | N | N | N |