| Variant ID: vg0800164418 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 164418 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GGAAGTCATTGTATGAAGAAGGGCAGACGTGTAGCATGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCGCGTC[A/G]
TCGGCAGACAACCGTGCTCCCACGATGCATCTGCCTCCGGTGGAGTGGAGGTAGGTATGACCCATCTCGTCGGATGGTCATTTGGATAGCAGCCATGGCA
TGCCATGGCTGCTATCCAAATGACCATCCGACGAGATGGGTCATACCTACCTCCACTCCACCGGAGGCAGATGCATCGTGGGAGCACGGTTGTCTGCCGA[T/C]
GACGCGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGCTACACGTCTGCCCTTCTTCATACAATGACTTCC
| 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 | 40.10% | 0.10% | 10.30% | 49.45% | NA |
| All Indica | 2759 | 18.20% | 0.00% | 11.60% | 70.21% | NA |
| All Japonica | 1512 | 87.40% | 0.10% | 1.19% | 11.38% | NA |
| Aus | 269 | 3.30% | 1.50% | 50.19% | 44.98% | NA |
| Indica I | 595 | 24.40% | 0.00% | 5.88% | 69.75% | NA |
| Indica II | 465 | 20.00% | 0.00% | 10.54% | 69.46% | NA |
| Indica III | 913 | 12.60% | 0.00% | 15.55% | 71.85% | NA |
| Indica Intermediate | 786 | 18.80% | 0.10% | 11.96% | 69.08% | NA |
| Temperate Japonica | 767 | 97.40% | 0.00% | 0.00% | 2.61% | NA |
| Tropical Japonica | 504 | 71.60% | 0.20% | 3.57% | 24.60% | NA |
| Japonica Intermediate | 241 | 88.40% | 0.00% | 0.00% | 11.62% | NA |
| VI/Aromatic | 96 | 17.70% | 0.00% | 7.29% | 75.00% | NA |
| Intermediate | 90 | 53.30% | 0.00% | 7.78% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0800164418 | A -> G | LOC_Os08g01250.1 | synonymous_variant ; p.Asp22Asp; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0800164418 | A -> DEL | LOC_Os08g01250.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |