| Variant ID: vg1218480566 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18480566 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCCATCTGCTGATAGCCCACCCATGCAGAGACGAGGTGCCAGATCCTCTTGGTGTATCTACAAGTGGCAACGTGGTGCAATGCCGTCTCAGTCTCGCGGC[G/A]
GCAAAGAGGGCAACAACCATTGTTCTGCCATCCCCTGGTCGCAAGCCGGTCTAAAGTCCAGACTCTGTTCTGAATGATGAGCCAAGCATGAAATTTGCAT
ATGCAAATTTCATGCTTGGCTCATCATTCAGAACAGAGTCTGGACTTTAGACCGGCTTGCGACCAGGGGATGGCAGAACAATGGTTGTTGCCCTCTTTGC[C/T]
GCCGCGAGACTGAGACGGCATTGCACCACGTTGCCACTTGTAGATACACCAAGAGGATCTGGCACCTCGTCTCTGCATGGGTGGGCTATCAGCAGATGGA
| 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 | 31.60% | 0.20% | 5.31% | 62.95% | NA |
| All Indica | 2759 | 17.00% | 0.00% | 6.09% | 76.88% | NA |
| All Japonica | 1512 | 43.50% | 0.50% | 4.30% | 51.65% | NA |
| Aus | 269 | 89.20% | 0.00% | 2.60% | 8.18% | NA |
| Indica I | 595 | 9.40% | 0.00% | 4.37% | 86.22% | NA |
| Indica II | 465 | 13.80% | 0.00% | 3.66% | 82.58% | NA |
| Indica III | 913 | 22.30% | 0.00% | 9.20% | 68.46% | NA |
| Indica Intermediate | 786 | 18.60% | 0.00% | 5.22% | 76.21% | NA |
| Temperate Japonica | 767 | 60.60% | 0.00% | 1.83% | 37.55% | NA |
| Tropical Japonica | 504 | 26.40% | 0.20% | 7.94% | 65.48% | NA |
| Japonica Intermediate | 241 | 24.90% | 2.90% | 4.56% | 67.63% | NA |
| VI/Aromatic | 96 | 77.10% | 0.00% | 7.29% | 15.62% | NA |
| Intermediate | 90 | 55.60% | 0.00% | 4.44% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218480566 | G -> DEL | LOC_Os12g30780.1 | N | frameshift_variant | Average:6.845; most accessible tissue: Minghui63 young leaf, score: 11.521 | N | N | N | N |
| vg1218480566 | G -> A | LOC_Os12g30780.1 | missense_variant ; p.Arg149Cys; MODERATE | nonsynonymous_codon ; R149C | Average:6.845; most accessible tissue: Minghui63 young leaf, score: 11.521 | unknown | unknown | DELETERIOUS | 0.04 |