| Variant ID: vg1012224061 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12224061 |
| Reference Allele: G | Alternative Allele: A,T |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGTGAGCAGGAGGCGGCTGCGCGCAAGGCCGGCAACGGCGGTGCGGAGCGCGAGCAGGATGTGGCCGTGCGCGAGAAGGCTGTTGAACGCTGGCCGGTAC[G/A,T]
AGGCTTGCTGCGGCCGCTGGTCGCTGGGTCTCGCCGGTATACCTACATATCCATGATCCTGGGTCTCGCAATGCACGGCCGCGGCGAGGATGCCCTGTCT
AGACAGGGCATCCTCGCCGCGGCCGTGCATTGCGAGACCCAGGATCATGGATATGTAGGTATACCGGCGAGACCCAGCGACCAGCGGCCGCAGCAAGCCT[C/T,A]
GTACCGGCCAGCGTTCAACAGCCTTCTCGCGCACGGCCACATCCTGCTCGCGCTCCGCACCGCCGTTGCCGGCCTTGCGCGCAGCCGCCTCCTGCTCACG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 49.20% | 0.10% | 0.99% | 49.66% | T: 0.04% |
| All Indica | 2759 | 31.70% | 0.00% | 1.59% | 66.73% | NA |
| All Japonica | 1512 | 89.70% | 0.00% | 0.00% | 10.25% | NA |
| Aus | 269 | 11.50% | 1.90% | 0.74% | 85.87% | NA |
| Indica I | 595 | 12.30% | 0.00% | 1.85% | 85.88% | NA |
| Indica II | 465 | 39.40% | 0.00% | 2.37% | 58.28% | NA |
| Indica III | 913 | 35.20% | 0.00% | 1.42% | 63.42% | NA |
| Indica Intermediate | 786 | 37.80% | 0.00% | 1.15% | 61.07% | NA |
| Temperate Japonica | 767 | 97.40% | 0.00% | 0.00% | 2.61% | NA |
| Tropical Japonica | 504 | 81.90% | 0.00% | 0.00% | 18.06% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 0.00% | 18.26% | NA |
| VI/Aromatic | 96 | 10.40% | 0.00% | 0.00% | 89.58% | NA |
| Intermediate | 90 | 58.90% | 0.00% | 1.11% | 37.78% | T: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012224061 | G -> T | LOC_Os10g23830.1 | missense_variant ; p.Arg52Leu; MODERATE | nonsynonymous_codon ; R52L | Average:13.774; most accessible tissue: Callus, score: 51.074 | unknown | unknown | TOLERATED | 1.00 |
| vg1012224061 | G -> A | LOC_Os10g23830.1 | missense_variant ; p.Arg52Gln; MODERATE | nonsynonymous_codon ; R52Q | Average:13.774; most accessible tissue: Callus, score: 51.074 | unknown | unknown | TOLERATED | 0.30 |
| vg1012224061 | G -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:13.774; most accessible tissue: Callus, score: 51.074 | N | N | N | N |