| Variant ID: vg0128724191 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28724191 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTCCGAATGACCCTCCGATGGGATGGGTCATACCTACCTCCACTTCGCTGGAAGCAGATGCAACGTGGGAGCACGGTTTGTCTGCTGATGACGTGACCGG[C/A]
GTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGTCGCACGTCTGTCCTTCTTCATACAATGACTTCTTTGCAATGGTTG
CAACCATTGCAAAGAAGTCATTGTATGAAGAAGGACAGACGTGCGACATGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGAC[G/T]
CCGGTCACGTCATCAGCAGACAAACCGTGCTCCCACGTTGCATCTGCTTCCAGCGAAGTGGAGGTAGGTATGACCCATCCCATCGGAGGGTCATTCGGAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.70% | 1.40% | 4.97% | 27.00% | NA |
| All Indica | 2759 | 57.80% | 1.00% | 2.90% | 38.24% | NA |
| All Japonica | 1512 | 87.10% | 0.70% | 1.92% | 10.25% | NA |
| Aus | 269 | 48.30% | 7.80% | 41.26% | 2.60% | NA |
| Indica I | 595 | 50.30% | 0.20% | 1.18% | 48.40% | NA |
| Indica II | 465 | 51.60% | 0.00% | 1.29% | 47.10% | NA |
| Indica III | 913 | 68.00% | 1.50% | 3.40% | 27.05% | NA |
| Indica Intermediate | 786 | 55.50% | 1.70% | 4.58% | 38.30% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 64.90% | 2.20% | 5.36% | 27.58% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 0.83% | 4.56% | NA |
| VI/Aromatic | 96 | 46.90% | 2.10% | 9.38% | 41.67% | NA |
| Intermediate | 90 | 68.90% | 3.30% | 6.67% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128724191 | C -> A | LOC_Os01g49990.1 | synonymous_variant ; p.Gly28Gly; LOW | synonymous_codon | Average:10.888; most accessible tissue: Callus, score: 22.262 | N | N | N | N |
| vg0128724191 | C -> DEL | LOC_Os01g49990.1 | N | frameshift_variant | Average:10.888; most accessible tissue: Callus, score: 22.262 | N | N | N | N |