| Variant ID: vg1216387128 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16387128 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 90. )
AACTTGTCACCAACACTGGTGAATGCACCAATCAGCCCATCATCTTCAATTTCTTGTGTTCTGGCTTTCTTTGGCTTGCTTGCAGATGATGCCTCCCCAC[G/A]
ATCATCAGTAGTGGCAGGGCCATCATTTTCCTCTTCATCATTTTCAGTTTGGACATCCTCTGTTCCTAGGACTGAATTTGAGTCCTTTGCATACTTTCCC
GGGAAAGTATGCAAAGGACTCAAATTCAGTCCTAGGAACAGAGGATGTCCAAACTGAAAATGATGAAGAGGAAAATGATGGCCCTGCCACTACTGATGAT[C/T]
GTGGGGAGGCATCATCTGCAAGCAAGCCAAAGAAAGCCAGAACACAAGAAATTGAAGATGATGGGCTGATTGGTGCATTCACCAGTGTTGGTGACAAGTT
| 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 | 19.40% | 2.50% | 3.98% | 74.21% | NA |
| All Indica | 2759 | 2.90% | 0.40% | 2.28% | 94.45% | NA |
| All Japonica | 1512 | 53.00% | 5.50% | 3.77% | 37.70% | NA |
| Aus | 269 | 2.20% | 7.10% | 8.92% | 81.78% | NA |
| Indica I | 595 | 1.80% | 0.20% | 3.19% | 94.79% | NA |
| Indica II | 465 | 4.30% | 0.20% | 1.29% | 94.19% | NA |
| Indica III | 913 | 1.00% | 0.20% | 2.30% | 96.50% | NA |
| Indica Intermediate | 786 | 5.10% | 0.80% | 2.16% | 91.98% | NA |
| Temperate Japonica | 767 | 82.50% | 4.70% | 4.30% | 8.47% | NA |
| Tropical Japonica | 504 | 5.00% | 6.90% | 1.79% | 86.31% | NA |
| Japonica Intermediate | 241 | 59.80% | 5.00% | 6.22% | 29.05% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 40.62% | 56.25% | NA |
| Intermediate | 90 | 26.70% | 4.40% | 5.56% | 63.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216387128 | G -> DEL | LOC_Os12g27800.1 | N | frameshift_variant | Average:9.491; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg1216387128 | G -> A | LOC_Os12g27800.1 | missense_variant ; p.Arg474Cys; MODERATE | nonsynonymous_codon ; R474C | Average:9.491; most accessible tissue: Minghui63 panicle, score: 16.27 | unknown | unknown | DELETERIOUS | 0.05 |