| Variant ID: vg0802670291 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 2670291 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGGAGAAAGAGGTGGTTCACTTCGTTTGCCCCGTGAAACATAGAAGCACTGCATCGCTGTCAACCACAATAGTGCACGTGCTTTCCATCTCTTATAGTTT[G/T]
AACCATCAAAGGCATGTGGTTTCAGTGTAGCAGCAAAGCCAACTACCGAAAATGACCTTTCAGGTTTTTGGATTGTTGGAAATTTGGTCATAATTCGGCA
TGCCGAATTATGACCAAATTTCCAACAATCCAAAAACCTGAAAGGTCATTTTCGGTAGTTGGCTTTGCTGCTACACTGAAACCACATGCCTTTGATGGTT[C/A]
AAACTATAAGAGATGGAAAGCACGTGCACTATTGTGGTTGACAGCGATGCAGTGCTTCTATGTTTCACGGGGCAAACGAAGTGAACCACCTCTTTCTCCT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 74.90% | 0.30% | 1.69% | 23.11% | NA |
| All Indica | 2759 | 68.00% | 0.00% | 1.41% | 30.59% | NA |
| All Japonica | 1512 | 98.70% | 0.80% | 0.13% | 0.33% | NA |
| Aus | 269 | 4.50% | 0.00% | 11.90% | 83.64% | NA |
| Indica I | 595 | 97.00% | 0.00% | 0.00% | 3.03% | NA |
| Indica II | 465 | 83.90% | 0.00% | 0.86% | 15.27% | NA |
| Indica III | 913 | 43.90% | 0.00% | 1.86% | 54.22% | NA |
| Indica Intermediate | 786 | 64.60% | 0.00% | 2.29% | 33.08% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 97.60% | 1.60% | 0.20% | 0.60% | NA |
| Japonica Intermediate | 241 | 97.90% | 1.70% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 4.17% | 7.29% | NA |
| Intermediate | 90 | 84.40% | 0.00% | 3.33% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0802670291 | G -> T | LOC_Os08g05150.1 | N | stop_gained | Average:10.62; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0802670291 | G -> DEL | LOC_Os08g05150.1 | N | frameshift_variant | Average:10.62; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |