| Variant ID: vg0136519139 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36519139 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATTGACTAGCATCTTTTGTAGCATGTGTGGAGTAGTTTGTGGGTGTGTGGTATCCCATGGCAGTTGTGTCTCCCCATGGATGGAGAGGACCTTGTATATC[C/T]
TCAATGGTATCAATAACTTTCGTTACTGCTGCCCTTATCGCTATCTTAACTGCCGTTGTAATATTAGTCTTGAAAGCTCTCTTGAATAGGTTAGATGCGT
ACGCATCTAACCTATTCAAGAGAGCTTTCAAGACTAATATTACAACGGCAGTTAAGATAGCGATAAGGGCAGCAGTAACGAAAGTTATTGATACCATTGA[G/A]
GATATACAAGGTCCTCTCCATCCATGGGGAGACACAACTGCCATGGGATACCACACACCCACAAACTACTCCACACATGCTACAAAAGATGCTAGTCAAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.50% | 0.80% | 5.90% | 56.75% | NA |
| All Indica | 2759 | 4.50% | 0.00% | 5.62% | 89.89% | NA |
| All Japonica | 1512 | 95.90% | 2.30% | 0.13% | 1.65% | NA |
| Aus | 269 | 2.20% | 0.00% | 42.75% | 55.02% | NA |
| Indica I | 595 | 2.70% | 0.00% | 4.03% | 93.28% | NA |
| Indica II | 465 | 4.50% | 0.00% | 3.44% | 92.04% | NA |
| Indica III | 913 | 2.80% | 0.10% | 6.02% | 91.02% | NA |
| Indica Intermediate | 786 | 7.60% | 0.00% | 7.63% | 84.73% | NA |
| Temperate Japonica | 767 | 99.10% | 0.00% | 0.13% | 0.78% | NA |
| Tropical Japonica | 504 | 90.50% | 6.70% | 0.20% | 2.58% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.40% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 1.04% | 6.25% | NA |
| Intermediate | 90 | 65.60% | 2.20% | 6.67% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136519139 | C -> T | LOC_Os01g63040.1 | synonymous_variant ; p.Glu494Glu; LOW | synonymous_codon | Average:4.671; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0136519139 | C -> DEL | LOC_Os01g63040.1 | N | frameshift_variant | Average:4.671; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |