| Variant ID: vg1115079187 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 15079187 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCGATGGAAGCCGAGCGCAGCGCTGCCGTTGACGGAAGCCGGGTGTATCGTCGGATGCCGAATATGCCGCGTCGCGCCGCTGCCGCCGCCGCCGCTGGGC[G/A]
TAGCACTGCCTCCACCGCCGGACGCCCTATGCCATCGCCACCACACTACCACGTAGGCCAGGGCACAAAGCTGCCATCCAATGGGTTGTGGAGGTAATTA
TAATTACCTCCACAACCCATTGGATGGCAGCTTTGTGCCCTGGCCTACGTGGTAGTGTGGTGGCGATGGCATAGGGCGTCCGGCGGTGGAGGCAGTGCTA[C/T]
GCCCAGCGGCGGCGGCGGCAGCGGCGCGACGCGGCATATTCGGCATCCGACGATACACCCGGCTTCCGTCAACGGCAGCGCTGCGCTCGGCTTCCATCGA
| 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 | 41.30% | 0.10% | 27.91% | 30.66% | NA |
| All Indica | 2759 | 31.10% | 0.00% | 35.99% | 32.91% | NA |
| All Japonica | 1512 | 62.00% | 0.30% | 6.81% | 30.95% | NA |
| Aus | 269 | 25.30% | 0.00% | 68.40% | 6.32% | NA |
| Indica I | 595 | 21.80% | 0.00% | 27.23% | 50.92% | NA |
| Indica II | 465 | 33.10% | 0.20% | 44.30% | 22.37% | NA |
| Indica III | 913 | 32.60% | 0.00% | 40.31% | 27.05% | NA |
| Indica Intermediate | 786 | 35.00% | 0.00% | 32.70% | 32.32% | NA |
| Temperate Japonica | 767 | 73.00% | 0.30% | 7.17% | 19.56% | NA |
| Tropical Japonica | 504 | 51.00% | 0.40% | 6.94% | 41.67% | NA |
| Japonica Intermediate | 241 | 49.80% | 0.00% | 5.39% | 44.81% | NA |
| VI/Aromatic | 96 | 56.20% | 0.00% | 10.42% | 33.33% | NA |
| Intermediate | 90 | 41.10% | 0.00% | 32.22% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1115079187 | G -> A | LOC_Os11g26350.1 | missense_variant ; p.Arg13His; MODERATE | nonsynonymous_codon ; R13H | Average:19.034; most accessible tissue: Minghui63 panicle, score: 38.588 | unknown | unknown | TOLERATED | 0.48 |
| vg1115079187 | G -> DEL | LOC_Os11g26350.1 | N | frameshift_variant | Average:19.034; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |