| Variant ID: vg1012223948 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12223948 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGACGAGGTTGTCCACGGCAAGGGAGCGGGTAGCGGCGACCGCGCGCCAGGAGCGACCAATGGCGCGGATGCGGACACGGTCGGGGAGGGAGCGCGAGGA[C/T]
GGCGGCGTGGAGCGTGAGCAGGAGGCGGCTGCGCGCAAGGCCGGCAACGGCGGTGCGGAGCGCGAGCAGGATGTGGCCGTGCGCGAGAAGGCTGTTGAAC
GTTCAACAGCCTTCTCGCGCACGGCCACATCCTGCTCGCGCTCCGCACCGCCGTTGCCGGCCTTGCGCGCAGCCGCCTCCTGCTCACGCTCCACGCCGCC[G/A]
TCCTCGCGCTCCCTCCCCGACCGTGTCCGCATCCGCGCCATTGGTCGCTCCTGGCGCGCGGTCGCCGCTACCCGCTCCCTTGCCGTGGACAACCTCGTCG
| 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 | 49.80% | 0.10% | 0.72% | 49.34% | NA |
| All Indica | 2759 | 33.30% | 0.10% | 0.80% | 65.78% | NA |
| All Japonica | 1512 | 88.60% | 0.20% | 0.26% | 10.91% | NA |
| Aus | 269 | 11.20% | 0.00% | 2.60% | 86.25% | NA |
| Indica I | 595 | 14.10% | 0.20% | 1.01% | 84.71% | NA |
| Indica II | 465 | 41.50% | 0.00% | 1.51% | 56.99% | NA |
| Indica III | 913 | 37.00% | 0.20% | 0.33% | 62.43% | NA |
| Indica Intermediate | 786 | 38.70% | 0.00% | 0.76% | 60.56% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 0.26% | 3.91% | NA |
| Tropical Japonica | 504 | 81.90% | 0.20% | 0.20% | 17.66% | NA |
| Japonica Intermediate | 241 | 79.70% | 0.80% | 0.41% | 19.09% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 0.00% | 90.62% | NA |
| Intermediate | 90 | 61.10% | 1.10% | 1.11% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012223948 | C -> T | LOC_Os10g23830.1 | synonymous_variant ; p.Asp14Asp; LOW | synonymous_codon | Average:12.598; most accessible tissue: Callus, score: 51.074 | N | N | N | N |
| vg1012223948 | C -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:12.598; most accessible tissue: Callus, score: 51.074 | N | N | N | N |