| Variant ID: vg1012224094 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12224094 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AACGGCGGTGCGGAGCGCGAGCAGGATGTGGCCGTGCGCGAGAAGGCTGTTGAACGCTGGCCGGTACGAGGCTTGCTGCGGCCGCTGGTCGCTGGGTCTC[G/A]
CCGGTATACCTACATATCCATGATCCTGGGTCTCGCAATGCACGGCCGCGGCGAGGATGCCCTGTCTCTATTCGCCAGCATGCAACGAGCCGGCGTGACG
CGTCACGCCGGCTCGTTGCATGCTGGCGAATAGAGACAGGGCATCCTCGCCGCGGCCGTGCATTGCGAGACCCAGGATCATGGATATGTAGGTATACCGG[C/T]
GAGACCCAGCGACCAGCGGCCGCAGCAAGCCTCGTACCGGCCAGCGTTCAACAGCCTTCTCGCGCACGGCCACATCCTGCTCGCGCTCCGCACCGCCGTT
| 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% | 1.08% | 49.64% | NA |
| All Indica | 2759 | 31.70% | 0.00% | 1.63% | 66.65% | NA |
| All Japonica | 1512 | 89.70% | 0.00% | 0.00% | 10.25% | NA |
| Aus | 269 | 12.30% | 0.40% | 1.12% | 86.25% | NA |
| Indica I | 595 | 12.30% | 0.00% | 2.18% | 85.55% | NA |
| Indica II | 465 | 39.60% | 0.00% | 2.15% | 58.28% | NA |
| Indica III | 913 | 34.70% | 0.10% | 1.31% | 63.86% | NA |
| Indica Intermediate | 786 | 38.20% | 0.00% | 1.27% | 60.56% | 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 | 8.30% | 0.00% | 2.08% | 89.58% | NA |
| Intermediate | 90 | 58.90% | 2.20% | 1.11% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012224094 | G -> A | LOC_Os10g23830.1 | missense_variant ; p.Arg63His; MODERATE | nonsynonymous_codon ; R63H | Average:12.993; most accessible tissue: Callus, score: 37.216 | unknown | unknown | TOLERATED | 0.40 |
| vg1012224094 | G -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:12.993; most accessible tissue: Callus, score: 37.216 | N | N | N | N |