| Variant ID: vg0139407180 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39407180 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACTCGGTCTCAAGGTAGACAGACCGTTGGACGGCGTTGTCACGGAAGACGCCTTCGATGTCGCTCCACACGGTGAAGGCAGAGGCGCGGGGCTTGTAGAC[G/A]
ACGTCGAAGACGTTCTTGGCGATGGAGTTGTGCAGCCAATTGACCACGCAGTGATCCGCACGGCGCCACTCGGCAGTGCGGAGGTCGAGAGCGGGCGGCT
AGCCGCCCGCTCTCGACCTCCGCACTGCCGAGTGGCGCCGTGCGGATCACTGCGTGGTCAATTGGCTGCACAACTCCATCGCCAAGAACGTCTTCGACGT[C/T]
GTCTACAAGCCCCGCGCCTCTGCCTTCACCGTGTGGAGCGACATCGAAGGCGTCTTCCGTGACAACGCCGTCCAACGGTCTGTCTACCTTGAGACCGAGT
| 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 | 30.90% | 9.80% | 5.01% | 54.34% | NA |
| All Indica | 2759 | 1.80% | 16.50% | 7.65% | 74.05% | NA |
| All Japonica | 1512 | 90.60% | 0.10% | 0.33% | 8.99% | NA |
| Aus | 269 | 0.40% | 0.40% | 1.49% | 97.77% | NA |
| Indica I | 595 | 2.90% | 18.70% | 15.80% | 62.69% | NA |
| Indica II | 465 | 1.30% | 4.90% | 2.15% | 91.61% | NA |
| Indica III | 913 | 0.30% | 24.50% | 4.71% | 70.43% | NA |
| Indica Intermediate | 786 | 3.20% | 12.20% | 8.14% | 76.46% | NA |
| Temperate Japonica | 767 | 98.40% | 0.00% | 0.13% | 1.43% | NA |
| Tropical Japonica | 504 | 79.80% | 0.20% | 0.40% | 19.64% | NA |
| Japonica Intermediate | 241 | 88.40% | 0.00% | 0.83% | 10.79% | NA |
| VI/Aromatic | 96 | 1.00% | 1.00% | 8.33% | 89.58% | NA |
| Intermediate | 90 | 38.90% | 6.70% | 10.00% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139407180 | G -> A | LOC_Os01g67800.1 | synonymous_variant ; p.Val102Val; LOW | synonymous_codon | Average:8.934; most accessible tissue: Zhenshan97 flower, score: 19.041 | N | N | N | N |
| vg0139407180 | G -> DEL | LOC_Os01g67800.1 | N | frameshift_variant | Average:8.934; most accessible tissue: Zhenshan97 flower, score: 19.041 | N | N | N | N |