| Variant ID: vg0604193278 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 4193278 |
| Reference Allele: C | Alternative Allele: CA |
| Primary Allele: C | Secondary Allele: CA |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 300. )
TGGGATGTAACCTTGTTGGCGTTTGGGACTAGCTCCTGCAGCGATTTCATCCGCTCCGCTATCCTCTCCCTCCGAAGCTGAAAATAACATGAACAATACA[C/CA]
AAAAAGTTGAGAAGAAAAATGGAAATGTTGCTCAAGTTCCATTTATTTTTTGGTTGAAACTTGAAAGAGGCAGTAATAATTGTAAGATGATTTCGTGAAC
GTTCACGAAATCATCTTACAATTATTACTGCCTCTTTCAAGTTTCAACCAAAAAATAAATGGAACTTGAGCAACATTTCCATTTTTCTTCTCAACTTTTT[G/TG]
TGTATTGTTCATGTTATTTTCAGCTTCGGAGGGAGAGGATAGCGGAGCGGATGAAATCGCTGCAGGAGCTAGTCCCAAACGCCAACAAGGTTACATCCCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.60% | 43.30% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 27.20% | 72.70% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 22.00% | 77.80% | 0.17% | 0.00% | NA |
| Indica II | 465 | 35.70% | 64.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 26.20% | 73.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 27.20% | 72.60% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 68.90% | 31.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0604193278 | C -> CA | LOC_Os06g08490.1 | upstream_gene_variant ; 2716.0bp to feature; MODIFIER | silent_mutation | Average:39.659; most accessible tissue: Callus, score: 67.489 | N | N | N | N |
| vg0604193278 | C -> CA | LOC_Os06g08500.1 | intron_variant ; MODIFIER | silent_mutation | Average:39.659; most accessible tissue: Callus, score: 67.489 | N | N | N | N |