| Variant ID: vg1012224010 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12224010 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCGCGGATGCGGACACGGTCGGGGAGGGAGCGCGAGGACGGCGGCGTGGAGCGTGAGCAGGAGGCGGCTGCGCGCAAGGCCGGCAACGGCGGTGCGGAGC[G/A]
CGAGCAGGATGTGGCCGTGCGCGAGAAGGCTGTTGAACGCTGGCCGGTACGAGGCTTGCTGCGGCCGCTGGTCGCTGGGTCTCGCCGGTATACCTACATA
TATGTAGGTATACCGGCGAGACCCAGCGACCAGCGGCCGCAGCAAGCCTCGTACCGGCCAGCGTTCAACAGCCTTCTCGCGCACGGCCACATCCTGCTCG[C/T]
GCTCCGCACCGCCGTTGCCGGCCTTGCGCGCAGCCGCCTCCTGCTCACGCTCCACGCCGCCGTCCTCGCGCTCCCTCCCCGACCGTGTCCGCATCCGCGC
| 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 | 50.40% | 0.00% | 0.36% | 49.24% | NA |
| All Indica | 2759 | 33.80% | 0.00% | 0.51% | 65.64% | NA |
| All Japonica | 1512 | 88.80% | 0.00% | 0.00% | 11.18% | NA |
| Aus | 269 | 14.10% | 0.00% | 0.74% | 85.13% | NA |
| Indica I | 595 | 15.10% | 0.00% | 0.34% | 84.54% | NA |
| Indica II | 465 | 42.40% | 0.00% | 0.86% | 56.77% | NA |
| Indica III | 913 | 37.20% | 0.10% | 0.33% | 62.32% | NA |
| Indica Intermediate | 786 | 38.90% | 0.00% | 0.64% | 60.43% | NA |
| Temperate Japonica | 767 | 95.70% | 0.00% | 0.00% | 4.30% | NA |
| Tropical Japonica | 504 | 81.90% | 0.00% | 0.00% | 18.06% | NA |
| Japonica Intermediate | 241 | 81.30% | 0.00% | 0.00% | 18.67% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1012224010 | G -> A | LOC_Os10g23830.1 | missense_variant ; p.Arg35His; MODERATE | nonsynonymous_codon ; R35H | Average:13.424; most accessible tissue: Callus, score: 51.074 | unknown | unknown | TOLERATED | 0.27 |
| vg1012224010 | G -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:13.424; most accessible tissue: Callus, score: 51.074 | N | N | N | N |