| Variant ID: vg0139407120 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39407120 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GTTGCTTCAGCTTGGCGGTGTACTGCGTGATGGTCATGTCACCTTGATTGATCGAGCGGAACTCGGTCTCAAGGTAGACAGACCGTTGGACGGCGTTGTC[A/G]
CGGAAGACGCCTTCGATGTCGCTCCACACGGTGAAGGCAGAGGCGCGGGGCTTGTAGACGACGTCGAAGACGTTCTTGGCGATGGAGTTGTGCAGCCAAT
ATTGGCTGCACAACTCCATCGCCAAGAACGTCTTCGACGTCGTCTACAAGCCCCGCGCCTCTGCCTTCACCGTGTGGAGCGACATCGAAGGCGTCTTCCG[T/C]
GACAACGCCGTCCAACGGTCTGTCTACCTTGAGACCGAGTTCCGCTCGATCAATCAAGGTGACATGACCATCACGCAGTACACCGCCAAGCTGAAGCAAC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.60% | 11.30% | 6.01% | 53.11% | NA |
| All Indica | 2759 | 1.40% | 16.80% | 9.53% | 72.20% | NA |
| All Japonica | 1512 | 87.40% | 3.30% | 0.46% | 8.80% | NA |
| Aus | 269 | 0.00% | 1.10% | 1.49% | 97.40% | NA |
| Indica I | 595 | 2.40% | 18.80% | 21.18% | 57.65% | NA |
| Indica II | 465 | 0.60% | 4.90% | 2.58% | 91.83% | NA |
| Indica III | 913 | 0.20% | 25.10% | 5.37% | 69.33% | NA |
| Indica Intermediate | 786 | 2.70% | 12.70% | 9.67% | 74.94% | NA |
| Temperate Japonica | 767 | 98.40% | 0.00% | 0.13% | 1.43% | NA |
| Tropical Japonica | 504 | 70.60% | 9.30% | 0.60% | 19.44% | NA |
| Japonica Intermediate | 241 | 87.60% | 1.20% | 1.24% | 9.96% | NA |
| VI/Aromatic | 96 | 1.00% | 8.30% | 2.08% | 88.54% | NA |
| Intermediate | 90 | 41.10% | 7.80% | 8.89% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139407120 | A -> G | LOC_Os01g67800.1 | synonymous_variant ; p.Arg122Arg; LOW | synonymous_codon | Average:7.802; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0139407120 | A -> DEL | LOC_Os01g67800.1 | N | frameshift_variant | Average:7.802; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |