| Variant ID: vg0234178765 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34178765 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 386. )
AACACCACCAGTTATGGAGCCACCGGCGGGTTCAGAAGCATCCGGCACTATGAGTGGGAGTGCATCGACGAACACCGGCTCAAAGAGATCAAGAACTTCC[G/T]
GTGTTTGGCAACATTTCGATGAGGTGGCCATGACAGGCCCTGATGGAAGGCAGGTAACATTCGCGAGATGTAGAATATGCAAAAATAAGTTATCTGCAAA
TTTGCAGATAACTTATTTTTGCATATTCTACATCTCGCGAATGTTACCTGCCTTCCATCAGGGCCTGTCATGGCCACCTCATCGAAATGTTGCCAAACAC[C/A]
GGAAGTTCTTGATCTCTTTGAGCCGGTGTTCGTCGATGCACTCCCACTCATAGTGCCGGATGCTTCTGAACCCGCCGGTGGCTCCATAACTGGTGGTGTT
| 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 | 79.70% | 0.20% | 8.21% | 11.96% | NA |
| All Indica | 2759 | 69.80% | 0.00% | 10.58% | 19.64% | NA |
| All Japonica | 1512 | 95.60% | 0.40% | 3.31% | 0.73% | NA |
| Aus | 269 | 91.40% | 0.00% | 7.81% | 0.74% | NA |
| Indica I | 595 | 45.00% | 0.00% | 15.80% | 39.16% | NA |
| Indica II | 465 | 66.90% | 0.00% | 13.76% | 19.35% | NA |
| Indica III | 913 | 86.90% | 0.00% | 5.15% | 8.00% | NA |
| Indica Intermediate | 786 | 70.40% | 0.00% | 11.07% | 18.58% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.52% | 1.17% | NA |
| Tropical Japonica | 504 | 91.70% | 1.20% | 6.94% | 0.20% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.00% | 4.56% | 0.41% | NA |
| VI/Aromatic | 96 | 79.20% | 2.10% | 17.71% | 1.04% | NA |
| Intermediate | 90 | 81.10% | 0.00% | 8.89% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234178765 | G -> T | LOC_Os02g55830.1 | missense_variant ; p.Gly69Cys; MODERATE | nonsynonymous_codon ; G69C | Average:5.822; most accessible tissue: Minghui63 panicle, score: 16.27 | unknown | unknown | DELETERIOUS | 0.03 |
| vg0234178765 | G -> DEL | LOC_Os02g55830.1 | N | frameshift_variant | Average:5.822; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |