| Variant ID: vg1107678718 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 7678718 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AACATATGGGATAATTCAGTGCTGACAAAAGGGCAACTCTACTATAGCACAGCTGATAAAGGTGGCATTTAAAGGACATCTATTGTTATCTTGACGTTGG[G/A]
TGGCTTGTAGAAGTGAAAGATGCAAACTGAATGGAGATGAATGGCATTGGTTGCTGCAAAAGTTGCCCATCCTCTCTTTAGGTTGCAACGATCGTCCGAT
ATCGGACGATCGTTGCAACCTAAAGAGAGGATGGGCAACTTTTGCAGCAACCAATGCCATTCATCTCCATTCAGTTTGCATCTTTCACTTCTACAAGCCA[C/T]
CCAACGTCAAGATAACAATAGATGTCCTTTAAATGCCACCTTTATCAGCTGTGCTATAGTAGAGTTGCCCTTTTGTCAGCACTGAATTATCCCATATGTT
| 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 | 41.80% | 0.20% | 8.17% | 49.79% | NA |
| All Indica | 2759 | 7.10% | 0.00% | 11.78% | 81.08% | NA |
| All Japonica | 1512 | 92.30% | 0.60% | 2.78% | 4.30% | NA |
| Aus | 269 | 89.60% | 0.00% | 4.09% | 6.32% | NA |
| Indica I | 595 | 4.90% | 0.00% | 12.10% | 83.03% | NA |
| Indica II | 465 | 3.90% | 0.00% | 7.53% | 88.60% | NA |
| Indica III | 913 | 4.60% | 0.00% | 13.25% | 82.15% | NA |
| Indica Intermediate | 786 | 13.70% | 0.00% | 12.34% | 73.92% | NA |
| Temperate Japonica | 767 | 96.60% | 0.00% | 0.91% | 2.48% | NA |
| Tropical Japonica | 504 | 92.10% | 0.00% | 4.76% | 3.17% | NA |
| Japonica Intermediate | 241 | 79.30% | 3.70% | 4.56% | 12.45% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 54.40% | 1.10% | 8.89% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1107678718 | G -> A | LOC_Os11g13900.1 | missense_variant ; p.Pro223Ser; MODERATE | nonsynonymous_codon ; P223S | Average:5.775; most accessible tissue: Callus, score: 18.856 | unknown | unknown | TOLERATED | 0.59 |
| vg1107678718 | G -> DEL | LOC_Os11g13900.1 | N | frameshift_variant | Average:5.775; most accessible tissue: Callus, score: 18.856 | N | N | N | N |