| Variant ID: vg1120445396 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20445396 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ACATCGATGAATAATTTAAGTGTTCGAAGATTCTGCATGGCTCCTTGTGCAAACTCGATCTCCATGGTGTCACTCCAGTACTCGAAAAGTGATAGGCACT[T/G]
GAATCGGTAGCTGATTATCAGCCTCTCATCCCTGTCCACTGTGGGTTTCTCCACTCCTAGATAGAGACGACTAAGAGATGGTATGCTCCCAAGTATTTGC
GCAAATACTTGGGAGCATACCATCTCTTAGTCGTCTCTATCTAGGAGTGGAGAAACCCACAGTGGACAGGGATGAGAGGCTGATAATCAGCTACCGATTC[A/C]
AGTGCCTATCACTTTTCGAGTACTGGAGTGACACCATGGAGATCGAGTTTGCACAAGGAGCCATGCAGAATCTTCGAACACTTAAATTATTCATCGATGT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.30% | 0.10% | 0.40% | 21.20% | NA |
| All Indica | 2759 | 70.70% | 0.00% | 0.54% | 28.78% | NA |
| All Japonica | 1512 | 95.00% | 0.20% | 0.07% | 4.70% | NA |
| Aus | 269 | 55.80% | 0.00% | 0.74% | 43.49% | NA |
| Indica I | 595 | 52.90% | 0.00% | 0.84% | 46.22% | NA |
| Indica II | 465 | 79.40% | 0.00% | 0.65% | 20.00% | NA |
| Indica III | 913 | 71.30% | 0.00% | 0.66% | 28.04% | NA |
| Indica Intermediate | 786 | 78.20% | 0.00% | 0.13% | 21.63% | NA |
| Temperate Japonica | 767 | 96.60% | 0.00% | 0.00% | 3.39% | NA |
| Tropical Japonica | 504 | 90.50% | 0.60% | 0.20% | 8.73% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 1.04% | 12.50% | NA |
| Intermediate | 90 | 88.90% | 2.20% | 0.00% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120445396 | T -> DEL | LOC_Os11g34880.1 | N | frameshift_variant | Average:44.276; most accessible tissue: Callus, score: 85.408 | N | N | N | N |
| vg1120445396 | T -> G | LOC_Os11g34880.1 | missense_variant ; p.Lys498Gln; MODERATE | nonsynonymous_codon ; K498Q | Average:44.276; most accessible tissue: Callus, score: 85.408 | unknown | unknown | TOLERATED | 0.53 |