| Variant ID: vg0128509352 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28509352 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGCGCTATGTCCTGGGACTGGTACTGAGATCACGGTTTCGTAGGAAGCGGTTCGCGCCGTTTTTCCCACGACACGCTCCTGTCAGGTGCCGTTGTACGGC[G/A]
GTGCCAGATTGGGGTGTGACATATATGAACGATGGGAGGCGCGTGATGGTGGCGGTGTCTAGGCCGAACCTGGGCAGCGTCGGCTGCTGCTGCTCCTGCT
AGCAGGAGCAGCAGCAGCCGACGCTGCCCAGGTTCGGCCTAGACACCGCCACCATCACGCGCCTCCCATCGTTCATATATGTCACACCCCAATCTGGCAC[C/T]
GCCGTACAACGGCACCTGACAGGAGCGTGTCGTGGGAAAAACGGCGCGAACCGCTTCCTACGAAACCGTGATCTCAGTACCAGTCCCAGGACATAGCGCT
| 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 | 29.60% | 0.10% | 8.00% | 62.25% | NA |
| All Indica | 2759 | 6.80% | 0.20% | 9.39% | 83.62% | NA |
| All Japonica | 1512 | 75.70% | 0.00% | 1.52% | 22.82% | NA |
| Aus | 269 | 7.10% | 0.00% | 31.97% | 60.97% | NA |
| Indica I | 595 | 8.40% | 0.50% | 0.84% | 90.25% | NA |
| Indica II | 465 | 6.00% | 0.00% | 2.15% | 91.83% | NA |
| Indica III | 913 | 6.90% | 0.00% | 22.23% | 70.87% | NA |
| Indica Intermediate | 786 | 5.90% | 0.40% | 5.22% | 88.55% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.13% | 0.52% | NA |
| Tropical Japonica | 504 | 33.50% | 0.00% | 3.97% | 62.50% | NA |
| Japonica Intermediate | 241 | 88.40% | 0.00% | 0.83% | 10.79% | NA |
| VI/Aromatic | 96 | 16.70% | 0.00% | 4.17% | 79.17% | NA |
| Intermediate | 90 | 37.80% | 0.00% | 6.67% | 55.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509352 | G -> A | LOC_Os01g49570.1 | synonymous_variant ; p.Thr74Thr; LOW | synonymous_codon | Average:21.62; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg0128509352 | G -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:21.62; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |