| Variant ID: vg1216387240 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16387240 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGGCAGGGCCATCATTTTCCTCTTCATCATTTTCAGTTTGGACATCCTCTGTTCCTAGGACTGAATTTGAGTCCTTTGCATACTTTCCCGTAGCCATGGT[G/A]
CTACCAAATATTGTAAGCATCTCACCATAGTGTGCAAGAGGTTTGTTAAAATAATCAGCATCAGCCTTGTGATCCTTCGGTGAAACAAAATTTTTTTAAG
CTTAAAAAAATTTTGTTTCACCGAAGGATCACAAGGCTGATGCTGATTATTTTAACAAACCTCTTGCACACTATGGTGAGATGCTTACAATATTTGGTAG[C/T]
ACCATGGCTACGGGAAAGTATGCAAAGGACTCAAATTCAGTCCTAGGAACAGAGGATGTCCAAACTGAAAATGATGAAGAGGAAAATGATGGCCCTGCCA
| 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 | 54.80% | 0.00% | 26.72% | 18.47% | NA |
| All Indica | 2759 | 34.30% | 0.10% | 39.54% | 26.13% | NA |
| All Japonica | 1512 | 82.30% | 0.00% | 9.19% | 8.47% | NA |
| Aus | 269 | 91.10% | 0.00% | 4.46% | 4.46% | NA |
| Indica I | 595 | 23.70% | 0.00% | 58.82% | 17.48% | NA |
| Indica II | 465 | 31.60% | 0.00% | 32.47% | 35.91% | NA |
| Indica III | 913 | 43.50% | 0.10% | 29.35% | 27.05% | NA |
| Indica Intermediate | 786 | 33.10% | 0.10% | 40.97% | 25.83% | NA |
| Temperate Japonica | 767 | 90.40% | 0.00% | 7.43% | 2.22% | NA |
| Tropical Japonica | 504 | 70.40% | 0.00% | 11.31% | 18.25% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 10.37% | 7.88% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 67.80% | 0.00% | 21.11% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216387240 | G -> DEL | LOC_Os12g27800.1 | N | frameshift_variant | Average:5.247; most accessible tissue: Callus, score: 10.072 | N | N | N | N |
| vg1216387240 | G -> A | LOC_Os12g27800.1 | synonymous_variant ; p.Ser436Ser; LOW | synonymous_codon | Average:5.247; most accessible tissue: Callus, score: 10.072 | N | N | N | N |