| Variant ID: vg1205718847 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 5718847 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACGATCGGCGAGAAGTAAATAAACGTTCTTGAGATCCTGTTATTTTCAAAATTCCGATCACCTCGCCTCACGCGGAAGAGAAAAATCTTTGTAGGGCGGC[A/G]
CGGGCAAAGGCGGCTCAAGGCGGGACTGATGCCGCTTCCAGCGTGTCCCCTGCGGCGACCTCGACAGGAGTCGTGGTCGGTACTAAGGACTAGGAGGTGG
CCACCTCCTAGTCCTTAGTACCGACCACGACTCCTGTCGAGGTCGCCGCAGGGGACACGCTGGAAGCGGCATCAGTCCCGCCTTGAGCCGCCTTTGCCCG[T/C]
GCCGCCCTACAAAGATTTTTCTCTTCCGCGTGAGGCGAGGTGATCGGAATTTTGAAAATAACAGGATCTCAAGAACGTTTATTTACTTCTCGCCGATCGT
| 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 | 62.10% | 37.90% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 95.50% | 4.50% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 6.30% | 93.70% | 0.00% | 0.00% | NA |
| Aus | 269 | 62.80% | 37.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 94.90% | 5.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 93.30% | 6.70% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 10.30% | 89.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 2.60% | 97.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 1.20% | 98.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 4.20% | 95.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 36.70% | 63.30% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1205718847 | A -> G | LOC_Os12g10680.1 | intron_variant ; MODIFIER | silent_mutation | Average:20.078; most accessible tissue: Minghui63 panicle, score: 29.741 | N | N | N | N |