| Variant ID: vg1115079160 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 15079160 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGGAAGTTGCACGCAGCGCCGCCGCCGTCGATGGAAGCCGAGCGCAGCGCTGCCGTTGACGGAAGCCGGGTGTATCGTCGGATGCCGAATATGCCGCGTC[G/A]
CGCCGCTGCCGCCGCCGCCGCTGGGCGTAGCACTGCCTCCACCGCCGGACGCCCTATGCCATCGCCACCACACTACCACGTAGGCCAGGGCACAAAGCTG
CAGCTTTGTGCCCTGGCCTACGTGGTAGTGTGGTGGCGATGGCATAGGGCGTCCGGCGGTGGAGGCAGTGCTACGCCCAGCGGCGGCGGCGGCAGCGGCG[C/T]
GACGCGGCATATTCGGCATCCGACGATACACCCGGCTTCCGTCAACGGCAGCGCTGCGCTCGGCTTCCATCGACGGCGGCGGCGCTGCGTGCAACTTCCA
| 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 | 97.80% | 0.60% | 1.54% | 0.06% | NA |
| All Indica | 2759 | 98.40% | 0.80% | 0.80% | 0.04% | NA |
| All Japonica | 1512 | 96.30% | 0.30% | 3.24% | 0.13% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.00% | 0.50% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.00% | 1.30% | 1.53% | 0.11% | NA |
| Indica Intermediate | 786 | 98.70% | 0.60% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Tropical Japonica | 504 | 93.30% | 1.00% | 5.75% | 0.00% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.00% | 4.98% | 0.83% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1115079160 | G -> A | LOC_Os11g26350.1 | missense_variant ; p.Arg4His; MODERATE | nonsynonymous_codon ; R4H | Average:19.514; most accessible tissue: Minghui63 panicle, score: 42.799 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1115079160 | G -> DEL | LOC_Os11g26350.1 | N | frameshift_variant | Average:19.514; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |