| Variant ID: vg0137499575 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 37499575 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AAAAAACCAGAAGACGAACAAGATGGGTGAGTGAAAACTCGCGTTGAGAGATTGAATACAGCCACGACGGGTGAGAGACGAACCTGCGAGGGGGTCGGTT[A/G]
AACGACCACTTTGGAGGGGAAATAAGGTTTCCCCGAGATGGTTCTGTCTCCCCCATCTTACGGGGCCACTTCTTCTTGCGCTCCCCCTCGGGCTGCGATG
CATCGCAGCCCGAGGGGGAGCGCAAGAAGAAGTGGCCCCGTAAGATGGGGGAGACAGAACCATCTCGGGGAAACCTTATTTCCCCTCCAAAGTGGTCGTT[T/C]
AACCGACCCCCTCGCAGGTTCGTCTCTCACCCGTCGTGGCTGTATTCAATCTCTCAACGCGAGTTTTCACTCACCCATCTTGTTCGTCTTCTGGTTTTTT
| 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 | 29.00% | 0.10% | 5.56% | 65.30% | NA |
| All Indica | 2759 | 2.00% | 0.20% | 0.18% | 97.61% | NA |
| All Japonica | 1512 | 77.60% | 0.00% | 15.94% | 6.42% | NA |
| Aus | 269 | 0.70% | 0.00% | 2.23% | 97.03% | NA |
| Indica I | 595 | 0.30% | 0.00% | 0.00% | 99.66% | NA |
| Indica II | 465 | 1.70% | 0.00% | 0.00% | 98.28% | NA |
| Indica III | 913 | 1.00% | 0.30% | 0.44% | 98.25% | NA |
| Indica Intermediate | 786 | 4.70% | 0.30% | 0.13% | 94.91% | NA |
| Temperate Japonica | 767 | 73.00% | 0.00% | 19.69% | 7.30% | NA |
| Tropical Japonica | 504 | 91.90% | 0.00% | 4.37% | 3.77% | NA |
| Japonica Intermediate | 241 | 62.70% | 0.00% | 28.22% | 9.13% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 8.33% | 2.08% | NA |
| Intermediate | 90 | 60.00% | 0.00% | 3.33% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0137499575 | A -> G | LOC_Os01g64610.1 | synonymous_variant ; p.Phe381Phe; LOW | synonymous_codon | Average:6.502; most accessible tissue: Callus, score: 16.181 | N | N | N | N |
| vg0137499575 | A -> DEL | LOC_Os01g64610.1 | N | frameshift_variant | Average:6.502; most accessible tissue: Callus, score: 16.181 | N | N | N | N |