| Variant ID: vg1012224060 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12224060 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCGTGAGCAGGAGGCGGCTGCGCGCAAGGCCGGCAACGGCGGTGCGGAGCGCGAGCAGGATGTGGCCGTGCGCGAGAAGGCTGTTGAACGCTGGCCGGTA[C/T]
GAGGCTTGCTGCGGCCGCTGGTCGCTGGGTCTCGCCGGTATACCTACATATCCATGATCCTGGGTCTCGCAATGCACGGCCGCGGCGAGGATGCCCTGTC
GACAGGGCATCCTCGCCGCGGCCGTGCATTGCGAGACCCAGGATCATGGATATGTAGGTATACCGGCGAGACCCAGCGACCAGCGGCCGCAGCAAGCCTC[G/A]
TACCGGCCAGCGTTCAACAGCCTTCTCGCGCACGGCCACATCCTGCTCGCGCTCCGCACCGCCGTTGCCGGCCTTGCGCGCAGCCGCCTCCTGCTCACGC
| 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 | 50.30% | 0.10% | 0.63% | 48.92% | NA |
| All Indica | 2759 | 33.50% | 0.00% | 0.83% | 65.64% | NA |
| All Japonica | 1512 | 89.10% | 0.40% | 0.33% | 10.19% | NA |
| Aus | 269 | 14.50% | 0.00% | 0.37% | 85.13% | NA |
| Indica I | 595 | 15.00% | 0.00% | 0.50% | 84.54% | NA |
| Indica II | 465 | 41.50% | 0.00% | 1.51% | 56.99% | NA |
| Indica III | 913 | 37.00% | 0.00% | 0.77% | 62.21% | NA |
| Indica Intermediate | 786 | 38.80% | 0.00% | 0.76% | 60.43% | NA |
| Temperate Japonica | 767 | 96.30% | 0.80% | 0.26% | 2.61% | NA |
| Tropical Japonica | 504 | 81.50% | 0.00% | 0.60% | 17.86% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 0.00% | 18.26% | NA |
| VI/Aromatic | 96 | 10.40% | 0.00% | 1.04% | 88.54% | NA |
| Intermediate | 90 | 63.30% | 0.00% | 0.00% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012224060 | C -> T | LOC_Os10g23830.1 | stop_gained ; p.Arg52*; HIGH | stop_gained | Average:13.774; most accessible tissue: Callus, score: 51.074 | N | N | N | N |
| vg1012224060 | C -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:13.774; most accessible tissue: Callus, score: 51.074 | N | N | N | N |