| Variant ID: vg1206302051 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 6302051 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGAGGCCATCACCGGCGCCTCCTGCAGCGCCGCCGCCATGACGAACAGCATCAGGACGAGCAGCGCCGCCAGCCGCCGCCGGCCACCGGTGGCCCTGAGC[G/A]
CCGCCGCCATCGCCGATCCTCCGATGATCCTTACTAACTAATTAAGCTACTTAACTGATTTGTCACAGATGTTTGGGTTAATCTGAATTTGCTGAAGGTT
AACCTTCAGCAAATTCAGATTAACCCAAACATCTGTGACAAATCAGTTAAGTAGCTTAATTAGTTAGTAAGGATCATCGGAGGATCGGCGATGGCGGCGG[C/T]
GCTCAGGGCCACCGGTGGCCGGCGGCGGCTGGCGGCGCTGCTCGTCCTGATGCTGTTCGTCATGGCGGCGGCGCTGCAGGAGGCGCCGGTGATGGCCTCC
| 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 | 39.90% | 4.00% | 11.76% | 44.35% | NA |
| All Indica | 2759 | 36.80% | 6.60% | 17.72% | 38.93% | NA |
| All Japonica | 1512 | 46.90% | 0.30% | 2.91% | 49.93% | NA |
| Aus | 269 | 13.00% | 0.00% | 2.97% | 84.01% | NA |
| Indica I | 595 | 86.40% | 0.00% | 1.51% | 12.10% | NA |
| Indica II | 465 | 20.40% | 6.90% | 25.38% | 47.31% | NA |
| Indica III | 913 | 11.90% | 12.40% | 26.51% | 49.18% | NA |
| Indica Intermediate | 786 | 37.70% | 4.70% | 15.27% | 42.37% | NA |
| Temperate Japonica | 767 | 57.10% | 0.00% | 4.30% | 38.59% | NA |
| Tropical Japonica | 504 | 27.00% | 0.80% | 1.59% | 70.63% | NA |
| Japonica Intermediate | 241 | 56.00% | 0.00% | 1.24% | 42.74% | NA |
| VI/Aromatic | 96 | 86.50% | 1.00% | 8.33% | 4.17% | NA |
| Intermediate | 90 | 47.80% | 3.30% | 7.78% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1206302051 | G -> DEL | LOC_Os12g11620.1 | N | frameshift_variant | Average:79.298; most accessible tissue: Zhenshan97 flag leaf, score: 87.567 | N | N | N | N |
| vg1206302051 | G -> A | LOC_Os12g11620.1 | missense_variant ; p.Ala4Val; MODERATE | nonsynonymous_codon ; A4V | Average:79.298; most accessible tissue: Zhenshan97 flag leaf, score: 87.567 | unknown | unknown | TOLERATED | 0.22 |